It means if he ever saw command again, it would likely be on an oiler in the North Sea or a fleet maintenance billet on Diego Garcia. He would likely get passed over a couple of times for promotion and after that, if he was smart, he would resign his commission and hope some corporation with less than scrupulous HR policies would pick him up.
As it is now, the military justice technicalities would likely be lost on someone in the private sector so he may be able to put this behind him, professionally that is. I doubt he'll get a good night's sleep any time soon, if ever.
Well now that the skipper is gone, looks like gilligan will sent in to turn around the boat.