After skimming that thread I agree that it does not suffer from the circlejerky problem. I also agree with your assessment that it is probably largely due to the subject matter and I think, additionally, that people in that thread's passion for the subject matter has an impact. I also agree that different (especially smaller and thus more intimate) sub-communities and sections will have less problem with this however if they are a smaller group in the first place they probably wouldn't have had problems with the old forums.
If we take the Live Balance sub-community, for example, if/when GD is removed people should go there to spout their "nerf Champion X, I swear its not just because I lost to one." In "discussions" like that good or different ideas that are not popular or suggestions that include nerfing said "Champion X" will get down-voted by a bunch of people playing said champion regardless of whether it is good/insightful (or it will be ignored and slip through the cracks never to be read by anyone). This is directly related to people posting the witty comments and other easily accepted responses that will be up voted and essentially drowning out the other responses.
I'm not saying there is no problems with the normal style of forums, because there obviously is, and they are in many respects similar to the problems posed around here in the Beta Feedback sub-forum for this new style. However, with this opportunity available while you guys are trying to improve this new style of forum's experience, I cannot help but wonder if there is even a way to fix these issues for either system? (Especially this new one since it is what you guys are working on.)