What to do...
In my view, if they refuse to represent a country when they are fighting, then they are fighting for their own cause, which could be anything. If they injure or kill in the process, that makes them criminals. If they are organized, then they are organized criminals. They don't have the right to be treated as POWs protected by the Geneva Convention if they don't adhere to it themselves. And THAT is even if they DO wear uniforms and carry a flag. Members of Al Quaida certainly do not. Those crooks in Gitmo deserve to be there.
And in my view, it is ideal punishment to lock them away. They wanted to die. Deny the enemy death.