Campaign progress is stored in config.cfg. This is not a very good place to put it I think. If you delete the config file to go back to all defaults then you lose your progress in the campaign and the config file is only written upon successfully exiting the game. If Nexuiz crashes then you would lose your progress.

I would suggest saving the data to some kind of save game file. Not like a .sav in Quake though as you don't need the game in play. The save game file could list the statistics for the campaign so far.

I know this is not a good defense but quake3 did it the same way and honestly most people should not need to delete their config.cfg. But you are right, this might be something to do after the bug fix release