The most interesting character in Assassin's Creed 2 is actually a minor supporting character: Sister Teodora, leader of the Venetian Courtesans. She was sent to a nunnery at a young age but soon left to form La Rosa Della Virtù, a bordello staffed by former nuns. Despite her profession, she still considers herself a nun, and despite still considering herself a nun, she is an Assassin.
One could see her status as an Assassin as proof that the group in Ezio's time has taken a more relaxed attitude towards those of faith. But Teodora's beliefs do not actually conflict with the Assassins'. In fact, the opposite is true. The Assassins apply logic as far as it can go, using it to choose who to kill for the betterment of society, but they can't predict the future. So ultimately they are committed to believing that their actions will have the intended outcome. The Assassins practice this secular form of faith, one unconcerned with anything supernatural, one that simply involves trust in an unknown. Teodora applies that very same practice to her religious faith. Instead of blindly accepting the established faith as true, she applies a rational mind to her religion and rejects the things about Catholicism that seem wrong. The result is her own church that combines the teachings of Catholicism that she agrees with (a belief in one god) with her own beliefs about the spiritual importance of sex.
Her bio describes her beliefs, "life in the cloisters was sterile and 'earthly', and that only in 'partnership with another' could one 'truly enter the arms of God.'" Her logic applies to her immediate concerns and things yield a tangible result that can be felt, which she explains to Ezio in terms of what she sees as the beneficial outcomes of the brothel: "Men must know how to love in order to reach salvation. My girls and I provide that to our congregation". She works towards the long-term goal of salvation for her congregation/customers, a goal that would not exist if not for her faith, but she goes about it in the most practical way that she can see. She fits in with the Assassins because she doesn't follow faith blindly.
The Assassins fight not against faith in general but against the establishment of faith in a ruling body because established faith seeks to suppress knowledge in order to remain established. Teodora is proof that rationalism and faith can coexist, but she is shunned by the church and considered a heretic. The church requires blind faith and blind fellowship, the Templars would force such things if given power and that is what the Assassins fight against.
At end of Assassin's Creed 2, Ezio becomes an official member of the Assassins. His induction takes place atop a high tower, and when it is over, his peers dive out the windows. Ezio's first act as an Assassin is to follow them in their apparent suicide. But by this point, they have earned his total trust and he theirs. So he follows them out the window, performing an act that symbolizes the Assassins' beliefs by mixing a new faith with rationality. This is an act that even Altaïr performed in the first Assassin's Creed in order to prove his dedication to himself: a leap of faith.
