1. We remain under civilian control, they make the decisions at the end of the day. If they want to ignore our advice, that's the way it goes. Don't like it, go find a tinpot country to take over in a military coup.
2. The wider point about the MoD is that it is the only Gov't department that has a mixture of long term strategic thinking and a day to day operational headquarters in the same place. We wouldn't allow the Dept of Health to run a Hospital out of it's headquarters, why does it make sense for the MoD to do so?
Hell, it might even satisfy the bloodlust for removing Admirals, Generals and Air Chief Marshals.....