and you know this how?
Because the President is not omnipotent nor a dictator. What agency are we talking about here, the FBI? The Director of the FBI is in charge, and everyone in the FBI reports to him. What about the Justice Department? The Attorney General is in charge, and everyone in the Justice Department reports to him/her.
There have been many instances in history, even recent history, where these Presidential appointees were fired for insubordination.