I dont know if i agree with your actions taken about the plot of AC2 because youre missing out on 3 which is amazing. I never let fictional stores like the ones in video games really affect me though
You have to remember that AC is simply a piece of good story-telling. It has more to do with being against the holders of power. Some conspiracy theorists would consider it more pro-Christian in that sense. According to AC lore, Jesus and the early Christians were executed by the Templars (the blokes you kill in AC2).
None of it's real. If you play the game actually accept the premise that two human orders have been killing each other for millennia, there is no hope for you.
That said, I haven't played AC2, nor do I intend to. I bought it because of the Revolutionary War theme. That and John de Lancie plays the protagonist's father. SCORE!!!