I usually do the "right" thing on the first playthrough of games. Then on the next playthrough I just do whatever... including killing all innocents and shooting my own guys or whatever. You know, just to see what happens.
Another thing to consider is that for some reason, I don't have a problem with beating people up and shooting a whole bunch of people and cops in Grand Theft Auto, yet this had a different feeling. I think what separates these two games is the fact that GTA is satire about the worst of society and Call of Duty is a reminder of what we see as being real life... especially nowadays when we've got this whole "fear the terrorists" mentality... which personally I feel is stupid considering that's what they want from us and what the name "terrorist" implies lol.