I would suspect that he will. This happened on his watch, like a ship having an accident at sea. He can't point to someone else and say that they failed. As you know, it doesn't work that way in the military.
This case brought discredit on the USN and was a national embarrassment. Firing the JAG would make exactly the kind of statement that needs to be made. The JAG corps need a major shakeup and change in culture.