For gameplay, anti-trolling and coding simplicity I would suggest the co-pilot gets control when:
Pilot seat is empty\dead
Pilot uses the menu system to hand control over (if he was injured, inept or something I don't know)
Co-pilot uses menu system when chopper is controlled by AI to take control, but only AI, not take control from a player.

Also to take loaded ammo from the rifle would be a great feature