I don't think that we should worry about this specific scenario. Any society advanced enough to develop mind uploading technology would have excellent understanding of the brain, consciousness and the structure of thought. In this circumstances retributive punishment would seem be totally useless as they could just change properties of the perpetrator brain to make him non-violent. and eliminate the cause of any anti-social behaviour.

It might be a cultural thing though, as america seems to be quite obsessed with retribution. I absolutely refuse to believe any advanced society with mind uploading technology would be so petty to use this in such horrible way . At that point I expect they would treat bad behaviour as a software bug.