I run a much less successful site than this and have dealt with and thought a lot about comment issues. HN does a brilliant job, for the most part, in handling comments. I would say that some people are unfairly hell banned (I see dead people) or slow banned, but it's for the greater good of the community and you can always get a new account.

My one possible suggestion would be to make HN more social. That way all the people who like to be trolls can troll each other and people not interested can unfollow, etc... Although, the Google+ Hacker News Circle has basically done this for me, and I like it a lot.