While the law requires that, acts of conscience contrary to orders will, in most cases, be career stalling if not court-martial launching. Further, you are insisting on an narrow and inflexible interpretation of events that others who viewed the movie clearly don't share. That the pilot didn't know about the tessaract doesn't alter the fact that the shot-callers were taking it into account.
A small tac-nuke would destroy a square kilometer of Manhattan, which is less area than the Avengers and Aliens had already trashed. As a result, it might well have been not only lawful under the rules of war, but arguably a road to fewer deaths in the final balance sheet. Destroy a kilometer of New York to end an alien invasion and turn the tide in a battle that was already taking down large buildings and killing thousands? A chunk of Manhattan vs. Planet Earth?
There are those who would consider not giving or following that order immoral. Its quite likely no one would give a damn about the pilot's man-in-a-foxhole moral quandaries - and prosecute him right into Leavenworth. Could it have been a non-nuke? Sure. But one that would take down Stark Tower would require a bomber and take longer to deploy. I'm not saying your are wrong, per se, but I am saying you don't have an interpretive monopoly on what to take away from that sequence.
And, in the end, we're arguing whether its realistic when Thor is fricking using his hammer like a helicopter blade?