Bush can simply not appoint a head of FDA. They say that the President has to obey the non-discretionary budget. Not true. The President can simply veto it. He can say here is a list of agencies I don't like and got to go. Send me a budget without apportioning for them and I will sign it. Otherwise, I will send the budget back to you. With Republicans in charge we can get rid of at least a few of the unwanted agencies.
In our dreams. Congress would override the veto in a heartbeat, with all the drug company lobbyists cheering as the votes to override come in.
Like I said, whether Republican or Democrat, our elected officials think they and the rest of the Washington bureaucracy are in loco parentis for the rest of us.