They're comparing inhumane treatment from the past to inhumane treatment from the past. Just because something used to be done doesn't mean it's acceptable. Also, just because something is better than what used to be done doesn't mean it's acceptable.
Justice should be fair. The punishment should not be worse for a trans person. I don't care what they did, it should be fair.
Consider this rule will also apply to someone who was arrested for something petty, like a drug charge or something. Should they also be tortured by being sent to the wrong prison? This is our chance to fix an issue with the system and maybe get Republicans on our side too. It's a win-win.
Either we're better people than then or we're not. It sounds like you aren't.