The morality in this series always cracks me up. The plot and the main character's cut scene actions never add up to ingame stuff, mass murdering thousands of guards/soldiers, because they're all evil, rite?
Even better, though, is when the developers talk about it. So you're an assassin, but that's not very politically correct, right, so of course you're murdering EBIL people only. 0:35, "your objective is to assassinate blabla, AND HELP BRING JUSTICE TO THE PEOPLE!!!!" and then you casually kill two soldiers because they were a slight inconvenience. None of it adds up, and it'd actually be a lot cooler from a story perspective if they stopped pussyfooting around, but I guess they can't since it's Ubisoft.