I'd prefer it if 'voting' went away entirely. I think you should be able to flag a comment as being hateful or abusive but that's it. The point of this site should be to read interesting articles, not focusing on the interaction of its commenting users.
In fact, i'd like it if you stopped displaying usernames too. Perhaps then people would actually consider all the comments instead of taking what one user says as gospel.
Actually.... I think that would solve most of the problems here. Remove score count and author name from a comment and all you have are two factors people consider: what got voted up to the top, and how many sub-comments are there on the parent comment. People will still vote up based on those two things (and how the comment looks/sounds) but that'll happen regardless.
I haven't read the Chronicle online but I imagine there isn't the same readership here. We can still flag or downvote based on abuse as long as everyone has to log into an account to comment. Thus you can ban accounts quickly, and the registration system can help identify duplicate or re-created accounts.
In fact, i'd like it if you stopped displaying usernames too. Perhaps then people would actually consider all the comments instead of taking what one user says as gospel.