Some religious leaders have said that this is not a just war. It clearly was not a war of last resort to prevent an imminent attack. However, if you were already deployed, as some were, would you have the knowledge and the willingness to take the consequences of refusing to follow your orders?
Consider, as a pilot, you would be given coordinates to strike. Would you question if they were valid war targets?
It always seems a difficult thing to ask about any war. I was in college during the Vietnam War. Many of us knew ( or knew of) fellow high school students who did not go to college and were drafted. Many, especially earlier in the war, so no alternative. In college, almost all of us were against the war. The culture we were in supported that. ( In fact, your question made me think of Donovan's Universal soldier "who really was to blame".
Much older now, I worry that many pilots are also victims, who will suffer for what they have done who never considered the US could order war crimes - even though we have before.