It's not an unfixable mistake. The only thing distinctly roguey/thiefy about NIN is Mug. Change that to something else and you can split it from rogue and make it a classless job, so rogue can be reworked into thief. It wouldn't be a technically difficult change to make at all; the rough part would be giving it an identity and playstyle distinct from NIN and any of the other melee jobs.