Tough to do. Look at the problems he’s having with letting the Attorney’s go even those whose contracts had expired. Trying to clean it out would result in a lot of leaks from their friends and the media who has been getting the leaks for years would also go after Bush for cutting off their bread and butter. Most of the people involved are covered by civil service and that makes it next to impossible to do a quick clean sweep.
There would be a similar if you tried to clean up the State Department.
He knows what’s what and has gone around them to get what’s needed.