The Codex 20: Pagan faiths

I have studied the ancient pagan faiths that came before this more recent obsession with a single, divine creator. They seem to have focused more on the fundamental forces at play in the world around us and less on arbitrary moral rules...

The sun rises in the morning and sets in the evening. The tides ebb and flow. Grass grows, withers, dies, and then in time, emerges from the ground once more. The air turns warm then cools and back again. Some hidden energy keeps us fitted to the ground and pulls us back when we attempt to leave it.

Each of these movements was represented before by a god or goddess. Each force given face, but recognized as something distinct and powerful. Which is not to say there were not connections between these forces – a pantheon of individual spirits – of rules. Invisible hands guiding the progress of the world around us.

And so here there was an attempt to categorize, study, explain, and understand the way things work – even if it was flawed. But no more. Now we are asked to succumb to a far more simplified explanation. How naive to believe there might be a single answer to every question. Every mystery. That there exists a lone divine light which rules over all. They say it is a light that brings truth and love. I say it is a light that blinds us – and forces us to stumble about in ignorance.

I long for the day when men will turn away from invisible monsters and once more embrace a more rational view of the world. But these new religions are so convenient – and promise such terrible punishment should one reject them – I worry that fear shall keep us stuck to what is surely the greatest lie ever told.

Commentary: Here Altair has a moment of reflection as he compares the past pantheistic traditions with his eras abrahamic monotheism. It is a unique take on the concept of the ancient pantheist worldview. But still a generalisation. I think Altair (and perhaps Des and his team) is being slightly naive as he wistfully looks back longingly at the pantheism of older traditions.
The pantheist traditions surely have their own flawed ways of thinking. Some of the myths of the pantheist and polytheist faiths were justifications for the way a certain society was structured or at least a reflection. Take the constant misogyny throughout Greek myth. Pandora the first woman was made to punish man. The two principle characteristics we are given regarding her are her beauty and cunning. It was she who let loose all the suffering of the world upon mankind. This justifies the ill treatment of women in Athenian society. Then there is the myth of Heracles' conquering of Sparta and his sons ruling as the eternal foreign kings. This myth was used to lend legitimacy to the two ruling dynasties and to justify the subjugation of the Spartan slave class. Within the Poetic Edda is the tale of Heimdall's creation of man. Mankind is not created equal in this tale, but is created as three different castes: the jarls, the farmers and the thralls. Within this tale is a justification for slavery as the thralls are depicted as ugly base humans that are fit for nothing but manual labor. Hinduism has a similarly caste based creation myth. 
So, it seems the older pantheist and polytheist traditions too, had injustices built into their teachings. 
But just as they have their bad side, I can agree they do have a good side. But so does the Abrahamic monotheism that Altair is so critical of. 
Altair lived at a time of Sunni dominance and given their stressing of the sharia and community tradition over any academic scholasticism, it would seem to him that monotheism has too great a stressing on arbitrary laws. Afterall, he is a Nizari Ismaili: a follower of shi'aism. Its only natural he would prefer a more spiritual take on Islam. 
But even then, his own ability to look beyond the sharia is proof that one does have to be obsessed with petty rules to be apart of the abrahamic tradition. There are many sects within monotheism that show their capacity for spiritual expression of the world around them.
Altair has fallen into the trap of thinking that one tradition is better than the other. But in truth, the flaw that brings religious traditions towards supporting injustice are those who use them to control. 
Those who try to suppress ideas and promote others, who demand that one doctrine is superior to the other. Those who, when pushed enough, will abandon more subtle means and use force to destroy all opposition to their voice. 
I cannot say whether one tradition is better than the other. If nothing is true, then how can one be better than the other? And if everything is permitted then why stop people from believing what model of the world they wish, so long as they do not use it to obstruct the free will of others? I can understand the wisdom in valuing reason. But nonetheless, these religious traditions themselves are knowledge and knowledge is intrinsically valuable. 
And if people wish to structure their lives under a certain set of rules and traditions. Then what harm is being done? I see no contradiction between following religious traditions (no matter how arbitrary) and living a rational life.
The only time I would worry about someone leading a religious life is if it was a life enforced upon them by those who would control and exploit them. But then, I would worry about any thought process that was enforced upon anyone in such a way.
I cannot say whether I agree with Altair's assessment. But perhaps I am merely misinterpreting it.
The Assassins have certainly shown (with Teahdora in Assassin's creed II) that one does not need to abandon religion in order to be an Assassin. 
Nothing is true and everything is permitted, after all.