Oohhh... I can indeed see how that can become a problem. I'll add that to my to-do list, as I've seen some pretty elegant alternative Arduino bootloaders that don't clobber so easily. Strange, though, that it would have the ability to overwrite itself, especially by accident... :/
I just don't like requiring people to build funky hardware like an ICSP cable in order to mod their devices... it's like locking people out a la Microsoftism, IMO. If a guy has an Arduino board, and the project is called "MPGuino", I think they'd expect to be able to play with it on a whim