There's something to analyse about the philosophical frameworks the Templars use throughout the Assassin's Creed games that lends credence to their point maybe, assuming the nature of reality the franchise utilises in its fictional universe is correct, anyway. The first game's post-assassination monologues offer the greatest insight into the philosophical grey area that later games tend to ignore, which is fascinating because technically speaking, the cosmology of the franchise presumably wasn't fully developed at the point in time the game was written, but it retroactively makes the Templars an ultimately sympathetic force, if an inherently flawed one.
After Altair assassinates Garnier de Naplouse early on in the first game, the Templar justifies his action by arguing that had he not imposed his control upon the will and minds of his patients, their lives would have been categorically worse (a consequentialist position that echoes the label commonly attributed to their faction, as in an aspiration for a Benevolent Dictatorship, or whatever form that would take in any given time period); altair points out that this still intrudes on their free will, but Garnier replies that such people as he took had little capacity for free will to begin with.
Even if Garnier is correct in this assessment, the Creed would still advocate for ultimate liberty in regards to such individuals, but the interesting part here is the discussion Altair has when he returns to Al Mualim:
Altair: Garnier de Naplouse is dead.
Al Mualim: Excellent! We could not have hoped for a more agreeable outcome.
Altair: And yet...
Al Mualim: What is it?
Altair: The Doctor insisted his work was noble. And looking back, those who
were supposedly his captives seemed grateful to the man. Not all of
them, but enough to make me wonder. How did he manage to turn enemy
into friend?
Al Mualim: Leaders will always find ways to make others obey them. And that is
what makes them leaders. When words fail they turn to coin. When
that won't do, they resort to baser things: bribes, threats, and
others types of trickery. There are plants, Altair, herbs from
distant lands, that can cause a man to take leave of his senses. So
great are the pleasures it brings, men may even become enslaved by
it.
Altair: You think these men were drugged, then? Poisoned?
Al Mualim: Yes, if it truly was as you describe it.
Altair: Herbs. This seems a strange method of control.
Al Mualim: Our enemies have accused me of the same.
Altair: The promise of paradise....
Given the twist ending of the game, the sophistry Al Mualim preaches in this conversation makes a lot of sense; Al Mualim himself has woven from the ideology of the Creed a false tapestry to pull over the Assassins' eyes, the means by which he controls and orders the Creed to do his bidding are inherently just as harmful and subjective as that of the Templars', it's predicated on a philosophical belief that may or may not accord with reality, and the merits of that accordance are very, very subjective, the individual Assassins just do not have the requisite information to make judgements of their own accord, it is a fundamentally authoritarian structure, self-justified by the oppression they face. Insodoing, the Creed under Al Mualim does more to harm their cause than the Templars, it's only when Altair takes over the order that this changes, his understanding of the pieces of Eden laying that foundation.
I'm getting ahead of myself though, under Altair's assumption that Al Mualim is in the right philosophically, and that the Creed really is acting in the name of liberty, one of his next targets highlight the hypocrisy once more, being that of Abu'l Nuquod:
Altair: If you do not serve Salahuddin's cause then whose?
Abu'l: In time you'll come to know them. I think perhaps you already do.
Altair: Then why hide? And why these dark deeds?
Abu'l: Is it so different than your own work? You take the lives of men and
women, strong in the conviction that their deaths will improve the lots
of those left behind. A minor evil, for a greater good? We are the same.
Altair: No, we are nothing alike.
Abu'l: Ah, but I see it in your eyes. You doubt. You cannot stop us. We will
have our new world.
When Altair returns to Al Mualim in the wake of this assassination, we get the following conversation, and it clarifies itself the issue of doublespeak that Al Mualim espouses, and I think it was specifically intended to get the player thinking about the Templar's true motives, much like Al Mualim's wish for Altair to do so, when the conversation itself is actually a masterful work of Al Mualim's deception, and he seems enthralled to be given the chance to bait Altair's temper with this paradox:
Al Mualim: Come, Altair. Speak with me a moment.
Altair: As you wish.
Al Mualim: Word has reached me of your success. You've my gratitude, and that
of the realm. Freeing these cities from their corrupt leaders will
no doubt promote the cause of peace.
Altair: Can you really be so sure?
Al Mualim: The means by which men rule are reflected in their people. As you
cleanse the cities of corruption, you heal the hearts and minds of
those who live within.
Altair: Our enemies would disagree.
Al Mualim: What do you mean?
Altair: Each man I've slain has confessed strange words to me. They are without
regret. Even in death they seem confident of their success. Though they
do not admit it directly, there is a tie that binds them. I'm sure of
it.
Al Mualim: There is a difference, Altair, between what we are told to be true
and what we see to be true. Most men do not bother to make the
distinction. It is simpler that way. But as an Assassin, it is your
nature to notice, to question.
Altair: Then what is it that connects these men?
Al Mualim: Ah, but as an Assassin, it is also your duty to still these thoughts
and trust in your master. For there can be no true peace without
order. And order requires authority.
Altair: You speak in circles, master! You commend me for being aware, then ask
me not to be. Which is it?
Al Mualim: The question will be answered when you no longer need to ask it.
This is where things get so hard to state succinctly, Al Mualim's words here on truth play directly into the series' maxim of 'Nothing is true, everything is permitted', while Ezio will later pontificate on these words, there's a wonderful amount of textual depth in the conversation above, because to anybody who is paying attention to what's actually being said, the philosophical qualms the order of Assassins should have with Al Mualim's stated position should go far deeper than the surface level commentary on authority and order:
Al Mualim is outright invoking what I would term an anti-realist position on the nature of knowable truth here, while some people are quick to jump to this as a 'postmodern' position on knowable truth, it's actually an analytical concept with a lot of precedence, if not providing much utility beyond its base assertions of knowledge being fundamentally unsure (even within experiential terms!), but Al Mualim's invocation is intentionally to be read as hypocritical, because the Assassins themselves are being lead entirely by what they've been told to do, who to kill, and for what ends, but any and all qualms one might have with the path being taken are stifled by the authoritarian structure, they literally can't abide by their position of seeing what is true, and in this way Al Mualim has taken great advantage of the structure. Again, the Assassins' trust in Al Mualim even as taking his actions as in the name of benevolence is no more subjective and debatable than that of the Templars' path to what they see as a better world, in fact, the point of the game is not that both paths are built on similar logical foundations, but that they are pursuing the same end with the same means. This does shift after Al Mualim is out of the picture, but that's where the idea of the Assassins' goals seem to become untenable as they are incongruous with the nature of reality as stated later on. I digress.
When Altair kills William of Montferrat, William's justification for his actions are arguably the strongest of the game; he is stowing food and supplies and forcing the populous to obey his strict laws because he is planning the distribution of such food around the harvest seasons, the structure he provides are presumed to objectively serve the populous better in the long run, even if some go hungry in the present. Altair fails to argue against it, and this is one of the major turning points for both his character and the narrative, though it doesn't seem like it at first. He has deposed a ruler that was simply enacting governmental planning in a wartorn region, and when he returns to Al Mualim his temper gets the better of him and he demands the truth.
All Al Mualim needs to say in order to still Altair's mind is that his enemies are all connected under the banner of the Templars.
That's all it takes, the learned enemy, the philosophical opposition to all Altair believes to be true and virtuous, these beliefs engrained into him since childhood, and he's ready to kill again.
Of course, Al Mualim betrays the order and Altair, whether he does it for purely personal gain or if he really believed in the creed but fell to temptation as a self-proclaimed benevolent dictator to the ends of freedom (much difference that does) is up for debate I think, but it's clearly in the wrong from Altair's perspective, heretical, even. So Al Mualim dies and the order thrives temporarily under Altair and we speed well ahead to the 15th century to assess how the structure of the universe applies to all of this.
Paradoxical as it is, the maxim 'Nothing is true, everything is permitted' touches on the aforementioned anti realist position, metaphysically, morally, even down to epistemology itself, but more than that, the idea of simulation theory, determinism, and though the Templars and assassins both believe in this maxim, they read it very differently, the Templars believe in the utilitarian power of illusion; it's best to impose order in spite of what truths may be, like the existence of god and miracles in the times of the crusades is very notable for the first entry, but the assassins on the other hand believe that ultimate and uncomfortable truth is always worth far more than the illusion.
This is where things get extra complicated because if we assess the fictional history and sci-fi elements of the franchsie we run into a lot of tripping points for a philosophical justification on either side, a quick rundown:
There once existed a precursor civilization that was looking to free itself from the constraints of time, realizing in their society's longevity that systems inevitably trended towards entropy, but within this pursuit they discovered that time itself was in some way analogous to code, or a program that the universe was playing through, a program that allowed a certain degree of variation between 'nodes' before inevitably collapsing toward pre-programmed events, events themselves that were invariably harmful to sentient life. 'Linear continuity is a simulation that allows for variations'.
This civilization decided that due to the deterministic state of the universe, and the fallibility of conscious entities' would-be attempts to change the inevitable, it would be best only to 'observe, not truly interfere' with the knowledge they had gleaned. This lead to their society becoming strict in an adherence to order, with knowledge of what was to come leading to a level of authoritarian stratification best suited to weather what may be around the corner; this too lead to the development of so-called 'eagle vision', an extra-sensory perception that when honed allows one glimpses of precognition, like a realization of the variables at play in the microcosm, a sort of interplay between conscious minds and the quoute unqoute 'simulation'.
Eventually time/the code itself reaches a state of complexity where it failsafe purges itself. nobody really knows why, but the implication is that when the universe becomes aware of itself as in humans, the knowledge of the true nature of time becomes a threat to itself, so mass extinction events on a universal scale occur, though due to the causal nature of time, it's presumed these events were accounted for by the universe well in advance.
With all of this in mind, one realizes that in actuality the series' main commentary is on the merits of this form of society with these facts taken into account. The precursor civilization realized that people are fundamentally irrational, and that information on the nature of existence not tempered by an authoritarian structure could only lead to bad outcomes; they lived through it, they tried the alternative, it didn't work. This is what the templars are repeating, at first out of self interest (they do not know what the pieces of Eden are, or their implications), but then out of a real metaphyical understanding. The Assassins reject this outlook precisely because they value that uncomfortable truth, this is what I meant when I talked about how the Templars and Assassins really shifting philosophically after Altair takes over, in a way that makes the Assassin's case for society weaker, it could be argued.
So in the case of Assassin's Creed 1, do we consider the Templars just in their attempts to consolidate power over the world via the pieces of Eden because they may be technically, inadvertantly correct in the most utilitarian way of approaching the nature of the universe? Or do we instead say that their reasoning is flawed and that regardless of the truth of this matter, intention is an important part of the equation? One might argue that consequentially people are better off because the level of happiness experienced by humanity as a whole across the entire timeline is greatly enhanced the earlier such control is gained by the Templars, but perhaps it's the case that society as a whole should come to a shared understanding of this fact, because it's free will in the balance. But then, does free will exist in a society where the universe is predetermined within a set of nodes that correlate directly with a sentient species' awareness of that very fact? Mind bending.
The nuance that does exist on the Assassin side of this equation seems to put forth the idea that even if the universe does work in this manner, people should come to their own conclusions, even if they are irrational/do harm. I don't know where I stand on any of this exactly, but intuitively I have to sympathize with the Templars, while recognizing that such truths of existence are inherently unfalsifiable until proof provides itself, and that allowing that personal autonomy under the Assassins' worldview is probably the right thing to do, but this allows the margin where Minerva/Juno/whoever appears to me in a hologram and tells me humanity is fucked, and I might have to make the call on that authoritarian control.
I don't know if I could do that, but then, would an Assassin? Al Mualim seemed to justify it even without this knowledge, I feel like in a sense, and the entire point of me writing this is coming to terms with the idea that the Assassins might actually just be wrong, and that fundamentally, a master Assassin of the brotherhood, if provided with this ultimate truth might have to reconcile this fact with the worldview and shift it accordingly.
A lot of people say this is why the true option is a 'middle ground'. The Templars may be correct in their assessment, but it doesn't justify immoral action to attain the control they seek, but then, if that immoral action is only done so because the Assassins are fighting against their ability to do so... Or hell, if gaining the pieces of Eden allows one to provide global happiness for a thousand years as a certainty, maybe great sacrifices towards that goal may be justified? You see how the fued between the two spirals and spirals, fighting from perspectives that are awkward to justify on multiple levels, but also speak to something real deep down. I have no idea, I really don't.