The loyalty question is not cut and dried. The president is the chief executive. There is no law-enforcement exception to this arrangement. Every executive-branch official, including the FBI director and the attorney general, is subordinate to the president. The president is in charge of executive-branch policy — of setting administration priorities for crime-fighting, intelligence-gathering, and much else. The FBI director does owe the president obedience in carrying out these priorities — just as FBI agents are bound to follow their director’s orders even if they privately question the prudence thereof. If the president decides that terrorism is the top of his agenda, the FBI director does not get to say he’s going to prioritize, say, health-care fraud.
There is a big difference, though, when it comes to the enforcement of law in particular cases. The FBI director, like all law-enforcement officers, takes an oath to uphold the laws of the United States. It is not a loyalty oath to the president. The rule of law demands that enforcement decisions be made based on what the Constitution and congressional statutes dictate, not on political considerations.
As a rule, the White House should not intrude in the conduct of investigations. Of course, there are exceptions. The pursuit of some cases might, for example, negatively impact foreign relations or national security. If a meritorious prosecution could touch off a crisis overseas or expose a life-saving intelligence operation, the president may have to kill it — especially if the executive-branch departments with skin in the game are divided on what should be done. That, however, is the extremely rare case. By and large, once enforcement priorities are set, politics should be walled off from investigations, which should go wherever the evidence leads.