"This brings us to the differences between legislative immunity and a pardon. They are substantial. The latter carries an imputation of guilt; acceptance a confession of it. The former has no such imputation or confession. It is tantamount to the silence of the witness. It is noncommittal. It is the unobtrusive act of the law given protection against a sinister use of his testimony, not like a pardon, requiring him to confess his guilt in order to avoid a conviction of it." - Burdick v. U.S. (236 U.S. 79)
Call it a wrongful conviction if you want. Witch hunt, whatever. By accepting the pardon Arpiao admitted his guilt. Plain and simple.
Interesting article on the subject here: https://reason.com/volokh/2017/08/26/is-accepting-a-pardon-an-admis
As with most legal rulings, the issue seems to be “complicated.”