Good point about the silliness of people downvoting Eliezer to show their disagreement.

Certainly, there are situations where replying to a negatively voted comment is the right thing to do. But are they the exception, or the rule? Because the new algorithm does not prevent you from doing this; it only provides a trivial disincentive to do so.

Using the phrase 'trivial disincentive' looks like a deliberate reference to this article which would be an unconvincing way to argue that the change won't cause any problems.

And in general, I don't think that the change will have really serious side-effects but I'm in favor of changing complex systems in as small increments as possible. The only sensible, currently relevant reason for implementing the new feature (flooding of the recent comments sidebar) that was given can be solved much less invasively by not having comments from crappy threads show up in the recent comments sidebar. For additional soft paternalist goodness, you could also have replies to comments made in such threads not appear in user's inboxes.

Do you think that visiting LW once in a week is enough to deal with that amount of information? Or do you just ignore most of that? How big part of a week can you spend online reading LW, and still pretending you are being rational instead of procrastinating?

Being able to keep up with all the conversation going on LessWrong seems incompatible with the goal of expanding the community. Reading comments and participating in conversation is a leisure activity. If I were very concerned with being "rational" about my LessWrong usage patterns I would stop reading them at all and stick to just articles (possibly only main section articles if I were really concerned).