If I recall correctly, all commissioned officers are issued a security clearance, is that correct?
If so, his should be revoked immediately.
Frankly, I think Mr. Trump should "go public" with this, as such:
Announce that Lt. Rapone has 48 hours to tender his resignation. If he does not do so within that allotted time, he should prepare to face Court Martial for treason.
Then see what happens next.
But... be prepared to remove this man from service if he won't go voluntarily.
Trump just won big with the "negro-kneeling" brouhaha.
He can roll another big win with the military by following up with the Rapone case.