There is only one real solution, which is to reduce size.
You can do that by closing new signups, which is a little bit like tying rope around a girls feet to prevent them from growing. Not great, and probably leading to rot.
Or you can do that by fragmenting up the conversations. Reddit has the rather primitive subreddit system. It works somewhat. A better system is Twitter's follow or Facebook's friend systems.
In either case, if you do this, the result would be something quite different from the old HN. The uproar would be great, and lots of people would leave.
The alternative is the slow death of online communities with scale. I just don't think that tweaks in the comment-karma system are going to solve this problem.
Good luck!