Are you saying that if we apply the laws impartially, for individual justice (as opposed to political gain), then all pardons and commutations are not valid? That seems like an extremely weird position to take.
I think all laws should be applied impartially. If they are not, and if an injustice occurs, then there are ways to correct that, from the prosecutor dropping a case...to the judge dismissing the case...to the jury nullifying the prosecution...to the appellate court setting aside a conviction...to the president commuting or pardoning the individual. I think all those things can exist under a system that prosecutes people justly for their crimes, instead of who those people are. So, your question seems out of place in this discussion.
Recently, Paul Manafort was prosecuted, but not his partner Podesta, because one was a Trump supporter and the other was not. If they committed the same crime (failing to register as a lobbyist), should only one be prosecuted because of his political allegiences, and the other not prosecuted because of his political allegiences? You give political support to people who do things like that (even though I assume you think that is wrong), so why can't I give political support to someone who will correct that injustice?
There is a long list of presidents pardoning and commuting sentences for bad people, even terrorists. Stones commutation is exceedingly mild in comparison. And, I think the president's power in that regard is absolute, as it was when Obama pardoned a terrorist, and commuted more sentences than the past 13 presidents combined.