Robert E. Lee famously refused to serve in the Union Army in a campaign against his own state of Virginia. He then resigned, left for the South, and joined the Confederacy.
Why was he, and other generals like him, allowed to do so? Wasn't it obvious they were going to join the war on the other side? Why weren't they interned or otherwise prevented to leave?
Officers serve on commission instead of contracts like enlisted members do and are free to resign at any time. Now officers must serve an obligated amount of time because their commissions are paid for by the government whereas in Lee's time you could purchase a commission or wait until you were promoted by merit or service which means that since it was your money the government wasn't losing anything financially by letting you resign. If you were promoted based on merit it was seen as already getting their money's worth.
It was obvious he was going to fight for the Army of Virginia and he stated that himself to make it very clear. Lee was morally opposed to slavery but felt he could not fight against his own state, something that was much more important then than it was now. Lee was also descended from the oldest family in Virginia so to fight for any northern Army would have been the worst form of treason.
That being said, while the legality of secession was debated then and now, resigning his commission, especially as a general officer, was entirely within his rights. What he did following his resignation really was of no concern of the Army's.