There are other choices lying in the continuum between "shoot him on the spot" and "give him a key to the city and send him on his way" ;)
In such a situation, I would have treated him as an agent of the enemy, and held him as a prisoner of war, rather than trying to take advantage of the criminal justice system. If they had good evidence that this guy was involved in such a thing, then he should be treated an agent of the enemy and a prisoner of war, same as in Quirin, and should have been on the next flight to Gitmo. But regardless of what we do with him, the ends cannot be used to justify the means.
I'm no lawyer, but prisoner of war status is for uniformed soldiers of organized military, not enemy agents in plain clothes working under cover. This guy was a saboteur and spy, or aided those who where. He doesn't deserve prisoner of war status. He deserves summary trial and execution, or a long prison sentence, just like the Nazi spies in WWII.