4. Of course, pardons have also been seen as having various other functions as well, such as decreasing the punishment of someone who is legally and morally guilty, for instance when “the situation and circumstances of the offender, though they alter not the essence of the offence, ought to make [a] distinction in the punishment” (Story’s words again). Sometimes the pardoning statement explains the pardoner’s reasons for the pardon; sometimes it doesn’t. And the beneficiaries of the pardon may of course disagree with the reasons given, even if they agree that a pardon is proper.
Legal authorities, then, are split on the subject of how the law should understand pardons; but because some pardons are understood as being based on the pardoned person’s factual innocence, I doubt that any judge today would genuinely view acceptance of pardon as always being an admission of guilt. And my sense (though I realize that it might be mistaken) is that most people’s moral judgment today would be that, even if a pardon is offered just as a gesture of mercy and not as exoneration, the recipient may honorably accept it even if they continue to deny their factual guilt or their moral guilt.