But the site is inherently real-time. Submissions pop onto and off of the front page in the course of a couple hours. The window for discussion is quite small before the next thing comes along. As it is, when I comment one something that's more than a few hours old, I halfway assume I'll never get a response/upvote/anything.
Just because a submission goes off the front page doesn't mean that nobody will comment on it anymore. Of course there will be fewer newcomers to the discussion, but people who are already in the thread will keep seeing it in their "threads" page so they can post replies even after a couple of days. Unless you post dozens of comments a day, it's relatively easy to keep track of threads that you're really interested in.
But that's part of the problem - comments will only show up if there are enough people looking at it to do the endorsing. A single site-wide list of pending comments won't work either - surely the whole point is that comments should be endorsed in the context of the thread?
It also runs the risk that things will only get endorsed if they agree with commonly-held views, and I'll also be interested to see how it effects things like whoishiring.
Some sort of moderation is fine, but I think that in its current implementation, this is a rather ham-fisted approach which will have a detrimental effect on HN.