I’m open to defining pardon more broadly. It always struck me as saying someone didn’t do anything wrong.
I believe that the President's pardon power was included in the Constitution in order to remedy injustices regardless of the degree of injustice. For that reason I would believe that the President would have the power to commute a sentence, reverse the findings of a federal court or a military court-martial, or even upgrade a dishonorable discharge to an honorable discharge.
The President can't change the facts of the case, but I think he has complete control over the outcome and can tailor his actions to the particular case.