I don't see my position as contradictory at all (big surprise, huh?).
The troops are in an impossible condition - precisely because they are undiciplined (in some cases) and jittery, yet they have been tasked with a role that they were not trained for. However, the fact that they have been put into a bad position does not excuse the poor judgement when it comes to taking other lives. I don't know what the answer is short of getting the hell out of Baghdad.