Looks like that idiot missed movement. Missing movement is in direct violation of Article 87 of the UCMJ, and the lieutenant put himself in jeapordy of being charged.
Will he be arrested? Probably not. There is historical precedent to deal with here, and officers are not normally arrested, except for the most heinous of offenses. I'm sure he had been restricted to Post, which any commander can impose almost at will.
Will he be Court-Martialed? That's up to him. He can admit guilt and avoid a trial, even though this one is a slam-dunk. The elements are pretty simple. Were I his commander, I would listen to the counsel of the SJA and charge him with everything I could think of. Article 90 certainly seems to apply and that carries the death penalty.
He is not a conscientious objector. He doesn't claim that his orders are illegal. Just that the war is illegal. The Army can certainly order him to get on an airplane. He doesn't get to pick his destination.
The Lieutenant has peed in his Wheaties. No doubt about that. As principled as he may think his stand is, a felony conviction and a dishonorable discharge will follow him for the rest of his life. Not to mention the total distain of every other officer who has ever sworn an oath.
The Army can't tolerate an officer who publicly disobeys lawful orders.