The president does not control the department of justice. It must follow the laws duly enacted. Historically, both parties have treated the justice department as an independent branch and avoided putting much public pressure on it. Breaking with that is one more way that Trump has damaged our republican democracy.
Which branch of government does the DoJ fall under? Hint: The Executive.
Who appoints the Attorney General? Hint: The President
Which cabinet does the AG sit on? Hint: The President's
Under the Executive Branch, who does the AG ultimately report too? Hint: The President.
As for your fantasy that "both parties have treated the justice department as an independent branch ", I guess you forgot about Eric Holder, who often referred to himself as Obama's "wingman". And maybe you forgot about Loretta Lynch and her infamous tarmac meeting with Bill Clinton?