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.

[1]http://paulgraham.com/trolls.html