Sounds great, but sounds as if either way you would lose.
If you upped the mission and noticed in-flight that he was acting up, chances are you already told him where you're headed. If you shoot him down using this new option most likely he will want revenge by switching sides and yelling, "BOMBER HORDE ON THE WAY AT COORDINATES ##,##. OVER ## BOMBERS!!!!"
Sure it would be nice, however there is a downside either way.