His C.O. should calmly pull him aside and inform him his work hasn't gone for naught. "We're withdrawing from Iraq starting with you son. Here's your dishonorable discharge, now get the hell off my ship."
He's not just against the war, he is against the military as an organization, in any form it may take. He enlisted to create hate and discontent. How far he gets is yet to be determined.
A real C.O. would issue a "Code Red" on this guy.