I'm on the last mission of the game, my second play through trying to get ghost and clean hands. Apparently, if you killed the assassins' in the prologue they count as kills which I don't think is fair because I figured you had to fight them off considering it's a semi rail moment. I can't actually remember if I killed them or not but I'm just so frustrated now because I feel like I wasted so much tedious time when I could have messed it up for myself from the very beginning. I don't think that it's fair and I don't think that killing those people in the begging should count, I mean think of it from a rational point of view: You're protecting the Queen and some guys come out of nowhere to kill her, simple taking them out will almost be an involuntary action. Maybe I'm reaching at this point, but I feel so angry and disappointed right now..

Nope, they do not.

There are a few other things that do though.