Some of the problem absolutely rests inside the DOD... but most of the real problem on the DOD side will get flushed out relatively quickly... there will be a new SECDEF, a new Deputy SECDEF, new SEC Army, SEC Navy, etc..etc.. all in place very soon.. Flag Officers appointed to positions that have been very politically vocal in favor of the outgoing party typically start retiring fairly quickly (they know their careers are over inside the pentagon and there is about to be a lot of competition for positions on the outside.. its better to be on the front of that wave than on the back side of it)..
There is absolutely a GS15/SES mafia inside the DOD of deeply entrenched bureaucrats that will be a whole lot harder to root out than the secretaries, under secretaries, deputy secretaries, etc.. but they arent nearly as much of a problem within the DOD as their cousins are inside DOS, DHS, DOJ, and other organizations in my experience..
My beef with many of the GS15 mafia within the DOD lies more in incompetence and laziness than it does with corruption or politicizing their positions like their cousins in the other departments, bureaus, and agencies..
Thats not to say they are all bad.. there are a lot of really good career civilians within the DOD... many that truly love their country, want to serve their country, and show up every day trying to do the best job they possibly can..
Unfortunately the public sector isnt like the private sector though.. and allows for a larger percentage of turds to permeate the proverbial punch bowl..