There, I think you get into whatever "individual" aspects are left. Some people still free lance, and can do it on reputation. As Armadillo says, there are exceptions. I know a few too, and they are dedicated and good people. And, as you point out, continuity is important in the DoD, as the DoD is unique amongst government agencies in having leadership turnover policy. GS, SES and actually nowadays, contractors provide that.
But to give my opinion on the question...man, I don't know. I have a good idea of what you are talking about. But in what little you have said, I'd guess this person has friends in high places. Best I can say, FWIW (being a planner) is if this person is truely an incompetent impediment - be sure first your goals are not contradictory to a bigger picture. Examine as many angles, and also their POV as much as you can. If you reach the same conclusions, very quietly develop a strategy with a plan and alternative plans to get what you want without harming them. Everyone has to save face. Vocal and visible is not a good tactic. Not saying you are, it just isn't. Works for news channel soundbites, but not in the real world.
Damn...I could write a lot on this, and probably doesn't sound like I made any sense at all. Just hard to get it down in a couple paragraphs.