People can also be nasty through PM's. Are we going to disable Pm's because of that? Frankly speaking, I don't think it's such a major issue. Few members started abusing the system, that does not mean there is something wrong with the system. One can abuse PM's as well.
Do we get so many complaints about rep messages? I have not seen a single one so far. So the Mods will be overworked because of handling negative reps does not have any basis as far as I know.