I'm going to resubmit an idea that has been brought up before (it's not mine- it may be yours, in fact): two buttons for voting. One for agreement/disagreement and one as a rating specifically for quality of the comment.

In the "old days," there was more-or-less agreement that the vote was for quality of comment -- feedback about the value of the participant to the community -- and agreement/disagreement was voiced (if necessary) in comments. As a rule I (and others) would upvote comments we disagreed with as long as they were thoughtful. There were exceptions, of course, as you have aknowledged, but this was a pretty good guideline.

Now I think things have turned around a bit, and votes have started signifying agreement/disagreement more than quality of comment. I think this takes the community in the wrong direction.