It was clear from some of John's earliest comments that he had been trained for terrorist actions, and that he had direct conact with al Qaeda training, camps and activities. I don't think any of that changes the argument much. He took up arms against his country, based upon his beliefs. Assuming he stands by those beliefs he will face the consequences of his actions. If he changes his stand, and either fights through legal means any court actions, or if he decides he was a victim of some powerful foreign brainwashing oranization, he will face the consequences of his actions based upon how well the court believes him.

If I were deciding his fate I'd decide how to proceed with his case depending upon how he cooperated and how strong a man of conviction I thought he was. The best he could for is a US Civil court, and I'd only go there if I was sure of the evidence and his level of cooperation.