Exactly, use the correct controller for the correct scenario. Keyboard+mouse works for many games, but for games where you control vehicles (racing games, aircraft simulators, submarines), joystick controls just work better.
Also, let's not forget that Microsoft would probably help out with hardening the security of the controllers. It's not like the Navy would have to reverse engineer the controller to figure out how to make it more secure.
This is the worst-case scenario for what is a rather overblown concern in the first place.
> I'm really more of a keyboard guy. Sometimes a mouse.
Even when operating a submarine?