Clemency is different from Justice; or rather, different from the legal system.
The goal of the legal system is to enforce the laws in an impartial manner. Whether Justice is achieved by that process depends on the content of the laws, in addition to the impartiality of their enforcement.
Since the Justice System is a human construction, it must be flawed. The purpose of the Clemency process is to allow for correction of flaws, some of which cannot be addressed in a practical way within the legal system. Since life is always a question of priorities, and priorities change over time, and the significance of events can sometimes be better seen in context, from a distance, Clemency allows for adjustment to actions that at once seemed clear and urgent, and later seemed doubtful.
It may be proper for employees of the Justice Department to think that Clemency is opposed to Justice; that is, to the work they do, but that is not so.