That's the inherent issue here. It's that the arrows used to represent quality in theory are actually used in practice to indicate agreement. And then with the down voting, you effectively have a system of negative reinforcement because your comments are being downvoted because you're a dissenter, but interpreted as a sign of bad quality and discouraged to speak further. It's interpreted as a sign of bad quality because all the signs say so. You get grayed out if it's too negative and your comment gets pushed to the bottom. Perhaps you'll become alienated and leave the community, making the HN community slightly more homogenous.
I agree with you in that it's a good idea to allow people to indicate their agreement and disagreement, but to have it clearly defined as an indicator of popularity.
I sometimes invite people to write such comments if they disagree with me. Often, when a comment makes a factual assertion for which I know of no evidence, I will reply to ask for the evidence. I will say things such as "Citations, please?" or "What are some examples of this?" or in some other way ask for the participant to back up the statement to which I reply.
But there are cases when a comment is totally wrong, and not a good contribution to the thread besides (which has always been a generally supported basis for downvoting), and it's just too much bother to post a countering reply or to ask follow-up questions. In such cases, I don't feel embarrassed at all in downvoting the wrong comment. The site founder pg, who announced news of changes he is considering in flagging options on HN in this thread, wrote 681 days ago,
I think it's ok to use the up and down arrows to express agreement. Obviously the uparrows aren't only for applauding politeness, so it seems reasonable that the downarrows aren't only for booing rudeness.
http://news.ycombinator.com/item?id=117171
Voting and flagging options today are still much as they were then, and so for the moment I don't think it's a bad idea to downvote for disagreement, particularly if a comment has other undesirable characteristics. I will happily adapt to a new system if the site management implements a new system. And I invite participants who disagree with this reply of mine to write a comment and explain why my argument is totally wrong, if that is not too much trouble to you.