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).
I don't think anyone at SI agrees with you about Less Wrong's mission. The site is supposed to be about rationality. There is hope (and track record) of the Less Wrong rationality community having helpful spinoffs for SI's mission, but those benefits depend on it having its own independent life and mission. An open forum on rationality and a closed board for donors to a charity aren't close substitutes for one another.