I will kill innocent NPC's if they deserve it (and if it won't alter the entire game). For example, I played a game recently (won't tell which one to avoid spoilers) that had an optional quest that required me to rescue a guy from captors. The quest has you rescue him but he is roughed up a little bit before you get to him. After you rescue him (in an optional quest, mind you) he gets mad at you for not showing up 5 minutes earlier. Well, after saving his life by my choice I decided to eliminate the non-grateful NPC. Hey, I know they are ones and zeros but I also know that a movie is just a movie. Part of the fun is letting go and getting involved in the story