You're right, the MOR discussion threads aren't very well organized for that. They work well enough for having an ongoing discussion, but not so well as an archive of the discussion that's already happened.
If you have a particular subject in mind and you want to see what's been posted about it, the simplest thing is probably to search the thread(s) for relevant keywords, including the chapter number. You could either use ctrl+f on each one of the threads that might contain relevant discussion, or the site's search function.
Don't worry so much about duplicating previous comments. It's worth doing a quick search to try to avoid it, but when it happens it's not so bad (especially with threads like these ones).
If you don't have a particular subject in mind and you just want to skim the discussion to see what's interesting, I don't have anything better to suggest than sorting by karma points.
Update: Discussion has moved on to a new thread.
The load more comments links are getting annoying (at least if you're not logged in), so it's time for a new Harry Potter and the Methods of Rationality discussion thread. We're also approaching the traditional 500-comment mark, but I think that hidden comments provide more appropriate joints to carve these threads at. So as of chapter 67, this is the place to share your thoughts about Eliezer Yudkowsky's Harry Potter fanfic.
The first 5 discussion threads are on the main page under the harry_potter tag. Threads 6 and on (including this one) are in the discussion section using its separate tag system. Also: one, two, three, four, five, six. The fanfiction.net author page is the central author-controlled HPMOR clearinghouse with links to the RSS feed, pdf version, TV Tropes pages, fan art, and more, and AdeleneDawner has kept an archive of Author's Notes.
As a reminder, it's often useful to start your comment by indicating which chapter you are commenting on.
Spoiler Warning: this thread is full of spoilers. With few exceptions, spoilers for MOR and canon are fair game to post, without warning or rot13. More specifically: