The President of the United States is the head of the Department of Justice as well as of every other departments, agency and branch of the executive government of the United States. As such, the President has the full constitutional and legal right to decide any and all decisions made by any part of the Justice Department or any other executive department.
As far as pardons, yes, I hope he gives a full, complete and immediate pardon to all victims of the Mueller witch hunt, the morning after election day, whether he wins or loses the election.