I've never liked the reputation system. It brings out the ugly in people. When they don't agree with the reputation you give them, they will 'attack.' It's just a number, and I'd rather get rid of it.
The reputation system is here to stay until Uzi says otherwise.
If any rep is abusive, just report it. If you get a negative, just PM the member that gave you it and see if you can figure out why/ how you can remove it.