Care to quote me where in the Constitution it allows a federal judge of a minor court to usurp Executive authority to pardon someone of a federal crime?
The Executive Branch's (Dept of Justice) own guidelines define the pardon as a forgiveness of the punishment, not the crime. (But of course, Trump ignored his own branch's guidelines and issued the pardon despite breaking several of the points of guidance.)
In any case, a pardon is an "expression of forgiveness," but does not remove the actual conviction. That's a separate issue, known as expungement. Others who have been pardoned still have the convictions on their record.
But of course, Joe Arpaio isn't supposed to be held to the law of everyone else, I know.