I *thought* negative rep points were to be used sparingly, and to express your disapproval of the tenor of someone's post, not so much of the poster or their opinions. If people are negative-repping others just because they don't like them, that would seem wrong, and perhaps neg. rep points are a problem.
On the other hand, I don't see anything wrong with people giving positive points to someone for posting an article they especially liked, or a well-written original piece, etc.
I was a moderator on a board that had a somewhat different type of points system, but like here, awarded by other members. Two people complained that unless everyone had equal points, some would "feel bad". Sounded kind of like psychological Socialism. Niot that that is what the problem is here, as I think we are all grown up enough here to not need that type of coddling.
If part of the sytem isn't working, address that, but don't throw the baby out with the bath water.