I've tossed this out a few times but what do you think about, say, the Fleet Admiral promotion being a mandatory (rather than optional) mission.
In that mission, we're roped into violating orders to save earth/the quadrant. And it's a serious violation, like violating the Prime Directive, the Temporal Prime Directive, something like that.
As a result, like Jim Kirk, we get busted down to a rank like Fleet Captain.
It falls into that category of the kinda of thing that it seems weird to consider everyone doing in an MMO. But any MMO is full of nquests or missions you can't think too hard about everyone doing (including our tutorial) and the net result would be Fleet Captain as the endgame rank. Might even lead to some interesting story possibility if we run into people who see us as a criminal or a hero depending on their stance.
And I think I would give players the option of following orders on that mission... But it would result in guaranteed death. The only way to survive would be to take the "rule breaking" option that gets you busted down.
After all, Captain is the TRUE rank of the star of the show is, NOT Admiral!!!! That would solve the thousands of Admirals out there flying a ship and scanning 5 rocks! Wow, what a great idea! Make Fleet Captain the end game rank! Brilliant! (And while you are at it, bust all your BO's who are Captains back down to Commander. (Why you would have Captains under you on the SAME ship is silly anyhow)
Just create a new rank called Fleet Captain. He has all the abilities and priveledges of a FA, just not a Admiral!