The President is the Executive branch. All others serve him and carry out his policies. They serve at his pleasure. Period. They do what they are told or should resign or be fired.Maybe a reason why Trump has trust issues with them? They don't like being kept in the dark.
Actually the "Deep State" of the State Department think they are the ones that actually run foreign policy and the elected politicians are just there to pay the bills and listen to lies that foggy bottom is doing what they are told to do....Who the fuck cares what State wants or doesn't want? They don't run the country nor do they set foreign policy.