(I'm not saying HN should do exactly the same thing, but one example is Slashdot's system where a comment can get downvoted in a way that tags it specifically as trolling/offtopic/whatever - https://slashdot.org/faq/mod-metamod.shtml seems to describe it alright)
I'd go the other way - disallow downvoting if you comment, and disallow comments if you downvoted. You get one choice of how to indicate that you don't feel the comment is correct.
Admittedly, teaching people not to downvote just for disagreement would be better. Personally, I downvote a ton, but never for disagreement - I downvote for exactly the reasons I see in the guidelines: non-substantive comments. Or, admittedly, I also downvote people who are just being a jerk.