I'm not so sure about that. The deeper the thread, the fewer participants, and the less benefit there is to the site as a whole. If karma is considered a measurement of that benefit rather than simply a score (as it should be, but on most sites that use the term is not), then it makes sense that threads with less participation would accumulate less in the way of extrinsic reward.

Also, consider that people so concerned with karma that they would be dissuaded from participating in a worthwhile discussion are among the least likely to have worthwhile discussions.