The "renegade pilots" idea is cool. Think of "The hurt locker".
In every armies there are commanders hated by many people in their unit for a reason or another.
I'm not reffering here at "The hurt locker", but There are asholes everywhere, and in the army if they have superior rank, this is really bad news for a lot of people.
I punched my sergeant flat on his back the first time I had a chance and i knew he won't rat about it. The a$hole jumped the fence and went in town to get few drinks. I was "Legally OFF DUTY".
He had to keep his mouth shut. I never again had to do two guard shifts every night, while the average was two shifts a week and run around the platoon for the seven kilometer march to the training grounds every day.
There were also many deserters that were hunted and shot down during the war.
This kind of tense relations are common in every army and is not a bad idea to have it in the game.