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).
Maybe have the comment threshold increase with the age of the comment. New comments should be visible at the current -1 threshold for a day or two but after that anything below 2 could be hidden. I think that immediately hiding comments would probably lead to fewer accurate comment ratings.
Another possibility is a user-selectable threshold.
We don't know how many people browse while they have sort set to New so you are right. Perhaps for comments older than a week or a month?