While I can certainly sympathise with you (things like what you described have happened to me too), I've learned my lessons and have become more rigorous at reviewing the IPTC stationary before applying it. I would strongly vote against it cleaning-up by default, however as this would not be preferable in almost all cases. Making it an option is all right, I guess though.
Note to Juerg: with one click on the "Clear" button in the IPTC stationary pad, all the previous settings will get erased. So maybe you could teach yourself to press this button every time you open the IPTC stationary? (you can actually specify which fields get cleared! While in the IPTC stationary window, press the "Option/Shift" key and the clear button becomes an "Options" button)
Kirk, if you intend to implement the requested "auto-clear" option, perhaps this option should honour the "Clear IPTC fields" settings as well. By the way, the "+" tick marks do not get cleared when you clear the fields with the clear button. Is this intentional or an oversight?