I'm personally against reputation systems in general, but perhaps there are ways to improve the one we have right now.
Consider, for example, that a negative reputation has to be reviewed by a moderator (or some other higher ranking member); the user giving the reputation must write a short note as to why the person in question deserves a negative reputation, and if the moderator thinks the negative reputation is well deserved, he passes it through. If a moderator has been given a negative reputation, another moderator will have to review it.
What do you guys think?