To address the Big Bad Threads problem specifically (as opposed to other problems), what we need is ability to close threads in some sense, but not necessarily as a side effect of voting on individual comments.
For example, moderators could be given the power to declare a thread (or a post) a Toll Thread, so that making a comment within that thread would start costing 5 Karma or something like that, irrespective of what you reply to or what the properties of your user account are. This would work like a mild variant of the standard (but not on LW) closed thread feature.
moderators could be given the power
By whom?
The recent implementation of a -5 karma penalty for replying to comments that are at -3 or below has clearly met with some disagreement and controversy. See http://lesswrong.com/r/discussion/lw/eb9/meta_karma_for_last_30_days/7aon . However, at the same time, it seems that Eliezer's observation that trolling and related problems have over time gotten worse here may be correct. It may be that this an inevitable consequence of growth, but it may be that it can be handled or reduced with some solution or set of solutions. I'm starting this discussion thread for people to propose possible solutions. To minimize anchoring bias and related problems, I'm not going to include my ideas in this header but in a comment below. People should think about the problem before reading proposed solutions (again to minimize anchoring issues).