The root of the problem is that the rating system is programmed as a measure of /comment quality/ while people use it as an "I agree" or "I disagree" which is something different entirely.

We could add a separate counter for "Agree/disagree" and "quality comment" but you'd still need the cultural change. You need your users to value quality comments, even if they disagree with the content of those comments. Looking at an argument you disagree with and seeing it's merits is a hard thing to do yourself; it's a very difficult thing to get other people to do.

If we want to change things, I think a better thing to look at is maybe making who voted publicly viewable? I know I quite often upvote people I argue with (I mean, if your comment is worth responding to, surely it is worth an upvote) and I think if they can see that I upvoted them, it sometimes inspires conversation rather than argument.