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.