Think of a baseball manager who doesn't get to hire his own coaches, or a football head coach who has assistant coaches forced on him by the GM. I don't think that sort of scenario usually works out well.
I agree if she’s so great why not let her head it up. or he might just want to make sure he has an insider keeping the spooks honest.
As you know, in business it is common to have to take on staff you inherit, but at least have major and veto say in new hirings, as well as, for cause, firings.
This is however a somewhat different animal, with political hires being more precarious.