I have to agree with Franklin on this one, Speed.
I personally got an officer(and pilot) removed from flight status and, ultimately, ended his career. He ended up being billed for his schooling at the Naval Academy, his flight school and other training when he requested(and received) a hardship discharge.
This was all due to him not following regulations and procedures:
1) Failing to use required safety gear.....Per Navy regs, when you are off the ground, be it on a ladder or on top of a aircraft, you are required to wear protective head gear to prevent injury in case of falling. The officer in question climbed the boarding ladder of one of my squadron's Prowlers without head gear
2) Before entering the cockpit, the ejection seat must be inspected for safety pins....The officer in question never checked for the safety pins. Worse still, he was about to enter the cockpit in the pilot's position. If the pilot's ejection seat is activated, all the other seats eject before the pilot's seat finally ejects, letting the pilot verify the rest of the crew got out as well as letting him keep the aircraft under control for the few seconds it takes for the other seats to eject. In this case, there were three of us occupying the other seats doing maintenance on the plane
3) You do not touch the ejection handles on a seat unless you need to eject.....This one should be pretty self-explanatory. In this case, however, the officer was using the windshield framing and ejection handle to get into the cockpit. Since the plane was in a hanger, had the seat not been pinned, he would have shot three of us into the hanger roof, probably taking our heads and legs off when going through the canopies as well
In this case, my reaction wasn't to report the incident but handle it directly. I told the officer to get off the plane before I threw him off bodily and, when he asked for my ID so he could report my communicating a threat and various other charges, I threw it across the hanger and told him to go get it if he wanted it that bad. A week later, there was a hearing to determine what charges would be held up and punishment given. The result was I ended up on probation for the next year while the officer was stripped of his flight qualifications and sent back to the training squadron to be retrained in how to board and fly a Prowler. Problem was that not one of the instructor pilots would fly with him and he eventually received his discharge, along with a bill for his training since he didn't fulfil his contractual obligations.
As far as JAG, they don't just cover officers. Did you ever see the movie "A Few Good Men"? That was about a pair of Marine enlisted men that got charged with a crime because they followed orders. AFAIK, JAG only gets involved when a capital offence is committed or when international law clarification is needed. Needless to say, IF you saw the series JAG, it was always a cut and dried major case and never anything that could be considered a grey area that could be handled by a ship/squadron CO. Had a guy in my squadron that was drunk on duty, more than once. Squadron CO sent him to rehab three times before he was booted for that and violating the "Don't ask Don't tell" protocol that also got four or five others booted with him. Jag wasn't even consulted as it wasn't a capitol offence.