While it complicates the interface, it would be much more useful for both authors and readers. It naturally leads to measuring controversy - the most interesting comments would be those with high quality and mixed agreement. Having a sense of HN's opinion would direct posts towards areas of maximum contribution. It would also re-direct some of the pile-on upvoting from low quality but obvious/funny/mean/etc. comments, so they could drop down the page despite having some appeal.
Some example cases: a) I may agree with the snarky comment that calls out someone's obvious mistake, but I can simultaneously downvote for snark. b) I may disagree with someone's analysis of the iOS vs Android market battle, but I can now register my disagreement while acknowledging that the poster made a good point. c) I made a comment that came off as means-pirited, though that wasn't my intent. The quality downvotes are an unambiguous message, which I can't just write off with "I guess HN disagrees."