I think that it isn't about incentivizing intelligent thoughtful conversation but rather disincentivizing the dumb or mean comments. People dislike losing karma a lot more than they like to gain karma. What pg observes in his article on Trolls[1], written a year before this one, is that controversial ideas which are modded down tend to be stubbornly left up while the wisecracks which are modded down tend to be deleted because there is less invested in them.
I try to make it a point to downvote any dumb/mean comments I see, even if I completely agree with the sentiment. If it's particularly mean or inflammatory, I'll also flag it.
Unfortunately, sometimes people sabotage that effort by upvoting said dumb/mean comments. I'd like to see a disincentive applied to those upvotes somehow. Like, perhaps, if a comment is flagged to death, deleted by a moderator, or results in a hellbanning, everyone who upvoted it should get a karma ding and a "please don't upvote mean or dumb comments like [quote of comment]" message.
[1]http://paulgraham.com/trolls.html