They'd be losing access to the most critical thing that makes them effective: the US military's logistics and chain of command. Without that they really are just some dudes with guns and a few fancy toys they won't be able to keep operational or replace. And they could never leave the state.
So as long as they aren't causing too much trouble ... just wait them out, then make an example of them in a military court.
And even then the code was far from the best it could be.
This guy optimized Super Mario 64 and drastically improved performance while fixing several bugs.