Another problem is that a reputation system might drive away people with valuable insights about certain agreed upon topics.
Relax, I doubt anyone with the ability to produce high-quality thinking is so insecure that (s)he'd be scared of getting a few downvotes on a website. (Myself, I once got an article submission voted to oblivion, but it just felt good in a feeling-of-superiority kind of way since I thought the LW community was the party being more wrong there -- though I think that to have found myself to be more wrong than I think I was would have felt good too.)
In general, I find it weird how some people manage to take the karma system so seriously. I thought it was acknowledged all along by the community that it's a very crude thing with only very limited usefulness (though still worth having).
Relax, I doubt anyone with the ability to produce high-quality thinking is so insecure that (s)he'd be scared of getting a few downvotes on a website.
I wouldn't be surprised to hear that the ability to produce high-quality thinking actually correlated with insecurity. People who spend time developing intellectual skills often neglect developing social skills, and a lack of friends/real social contact then makes them feel insecure.
People who go back and downvote every post or comment a Less Wrong user has ever made, please, stop doing that. It's a clever way to pull information cascades in your direction but it is clearly an abuse of the content filtering system. It's also highly dishonorable. If you truly must use such tactics then downvoting a few of your enemy's top level posts is much less evil; your enemy loses the karma and takes the hint without your severely biasing the public perception of Less Wrong's discourse.
(I just lost over 200 karma in a few minutes and that'll probably continue for awhile. This happens to me every few weeks. Edit: I mean it's been happening every few weeks for a few months for a total of only three or four. Between 400 and 700 karma lost total I think? I don't mean to overstate the problem.)