I took it into the Genius bar and they had nothing other than "we will wipe it and get it working."
It turned out I was able to boot to single user unix console mode and clean up the issue in an old school style. I have no idea if that is even possible anymore, but in any case I have never had another issue with OSX as severe as that one.
Modern Mac OS got really quite high quality at some point but it's easy for people to forget it had a lot of growing pains between 1999-2008 or so.