In the long run, he's still going to the stockade for a long time, because he DISOBEYED ORDERS. Doesn't matter if he took a stand based on his conscience or not; he very clearly DISOBEYED ORDERS given to him by superior officers, and that is why he will be convicted and serve time. 
 
That's just how the military works, BTW. You don't have to agree with your orders, but you do have to OBEY those orders.

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