A better system would have been to keep the reputation system in place, not worry about it, and if someone complains, they get banned or temp banned. Honestly, people shouldn't complain about such a thing in the first place.
Another way it could have been done, is instead of being able to take away reputation, you just EARN reputation. For example, if someone likes my post, they just give + rep. If they don't like the post, they just don't do anything and it stays at a moot point. That way, active members and members the community are fond of, can actually get what the system literally entails, "Reputation." Everyone else would have to earn reputation simply just by doing what they normally do in the community. If they keep doing something right constantly, or their posts are well thought out, then they would receive more rep, as they should. These people aren't going to complain about GETTING rep. In addition, someone who can't have reputation TAKEN AWAY can't get mad and moan and complain at their current reputation level. If their reputation level isn't going up, it would be because they aren't making interesting posts, or nobody actually cares about giving rep in that particular instance.
It seems like the fact that other users could "tarnish" another's rep was the root cause of your reputation system failure. If you had a system in place in which you just simply keep stacking up rep as you contribute something good, then there wouldn't be any problems. People would only have one thing to complain about, that they aren't GAINING rep... And that in itself is a silly thing to complain about, but the answer is obvious and self-serving, as if you're not gaining any reputation, then you're not making good posts, and you should try harder in the future. There shouldn't be a reason someone should PM Admins, Mods, etc for them not gaining any rep. In essence, it would be one's own fault.
I would think that, combined with a strict "don't pm us about rep" rule, would be able to keep the reputation system in place, and evolve it into something better.
But hey, that's just my two cents.
