Why do we want comment scores?
Because we want to be able to pick out quality comments quicker.
What is broken with comment scores?
They have created a motivation for people to try and game the comment scores. A simple way to do this is by writing polarizing comments, or kicking up an emotional debate. This hurts the comment system.
So what is the root problem? Why do people want to game the comment scores?
The reason people want to game the comment scores is because the comment scores are tied to their identity. If you can find a way to tie comment scores to the comments, and disconnect them from the user's identity, there should no longer be a motivation for people to game the comment scores.
So how can we do this? Here are a couple of my ideas.
1) Kill the current karma system and replace it with some new system. Why? Since karma is tied to comment scores, people don't just get the instant gratification of seeing their comment get voted up. They get to keep those points as long as they have the account. When you log in you see your karma score right next to your name, just begging you to try and raise it.
OR
2) After 10 upvotes (or some other chosen value) start fading the username from grey to green, and immediately replace that user's name on the entire page with a randomly chosen tag. It could be Alpha, or Liono, or characters from the 30Rock, doesn't matter. As long as it isn't directly tied to that user's identity anymore. If you replace the user's name with the same randomly chosen tag, then readers will still be able to see that that person's comments come from the same person, they just won't know who it is.
All I know for sure is that if comment scores come back they can't be tied directly to the user's identity.