In principle, the argument for an independent Justice Department seems at least as compelling as the argument for an independent Federal Reserve Board or Federal Communications Commission.
Consider the domain of criminal law enforcement, where the department has awesome and even terrifying power. It could take action against a president’s political enemies (“Lock her up”). Indeed, the mere possibility that it might do so could operate as a strong deterrent to criticism of the president — and so compromise democracy itself.
The department can also show leniency to a president’s political friends. The Roger Stone case is an example. Indeed, the very possibility that it will do so can create a strong incentive to become the president’s political friend.
The president’s power over the Justice Department is potentially even more dangerous than that. The department helps to oversee the antitrust laws, and in allowing or forbidding mergers, it can play political favorites. Civil actions, and not merely criminal ones, can be polluted by the president’s electoral interest (or spite).