It would probably be possible to initiate an AddToBlockIndex or Reorganize after the check, but it would require a lot more careful attention. I probably should break out part of AddToBlockIndex that sets the new best block. I'll probably end up doing that instead of the code below.
This is what I ended up doing in SVN rev 139.
Instead of deleting the bad chain, I added an extra CheckBlock to ConnectBlock so bad blocks can't get back into the best chain once they're kicked out.