This is another failure of leadership. In this case it mirrors the failure in leadership we saw after Tailhook (and yes I was there) when the senior civilian and uniformed leadership of the Navy failed to stand up for their people. The correct answer here was that Capt Honor has a sustained track record of getting the job done and is the best person to lead his ship on a deployment that he has trained them for. To fire him over this five years later is chickenshit and it appears that his crew backs him up on this (at least many have appeared in support)
So, the message is loud and clear to you young folks. The Navy will gladly sack you if you cross the line. No, they won't tell you where that line is and it moves.
Aside from the posters here who seem to be well in line with the PC party line I cannot in good conscious recommend a career in Naval Air to anyone anymore. Do a tour, two if you can get a second flying and then go own your own destiny. Do not ever think you are more than one anonymous complaint from being terminated.
I've told my son something similar - recently commissioned through ROTC and just starting in Information Warfare.