And if the senate or house is currently under the control of a party that opposes those actions?
In general, I think pardons are an imperfect solution to a problem, for which all alternatives are even more imperfect.
(Not that I wouldn't be opposed to seeing them modify the rules...)
I don't think there's anything wrong with pardons, and most Presidents have used them responsibly. But should any power of the President be absolute? It wouldn't diminish the interests of justice to establish some provision for Congress to revoke any particular pardon.