Which is why civilians have laws and soldiers have their orders: to overcome personal morality. That bomber pilot came back, so did the german fighter pilot, as would the ISIS fighter. Orders and laws recognize the bigger picture.
The structure operates both ways. We punish soldiers for applying their morality above orders because often that morality tells them to kill where their commanders don't want them too. In this case the soldier's moral code told him to disobey orders by not killing, but what about those situations where the soldier's moral code tells to disobey orders by killing? That leads to revenge, torture and all manner of illegal horrors ... which is why after WWII we setup a host of laws meant specifically to further usurp such decisions. The lesson was that, despite some noble stories, the decisions of gentlemen could no longer be trusted.
The structure operates both ways. We punish soldiers for applying their morality above orders because often that morality tells them to kill where their commanders don't want them too. In this case the soldier's moral code told him to disobey orders by not killing, but what about those situations where the soldier's moral code tells to disobey orders by killing? That leads to revenge, torture and all manner of illegal horrors ... which is why after WWII we setup a host of laws meant specifically to further usurp such decisions. The lesson was that, despite some noble stories, the decisions of gentlemen could no longer be trusted.