If they said "Yes, I know this is a crime, that it is wrong in many ways, but it is understandably a good choice under those circumstances", I wouldn't have such a problem.
This is actually pretty much what I say. It's a gigantic Necessary Evil, but hey, the Cylons have wiped out most of the human race and aren't showing signs of stopping, better safe than sorry and extinct.
But they act as if this was an undeniably right thing to do, and condemn Helo for doing the moral thing and refusing to commit a genocide. Even worse, they claim that he is a traitor for disobeying a direct order to commit genocide. I guess they must also think that the Nuremberg defense ("I was just following orders") was completely legitimate, eh?
Hey, a German who refused orders to kill Jews would
be a traitor. He'd also be doing the moral thing. These are not mutually exclusive, and by and large being a traitor to the Nazis is a more
moral thing than supporting them (for obvious reasons.)