Gun Drones are restricted by Threat Identification Protocols, true. There is no way to bypass it I'm aware of, apart from moving your Gun Drones in such a way as to make the thing you want to shoot the closest unit.
Now, Sniper Drones, Marker Drones, Interceptor Drones, and Missile Drones aren't restricted by that rule. So if they're using those drones, they don't have to worry about that rule.