This seems to have worked well for stack overflow. Just spitballing here pg, but what if you extended this to commenting as well? HN could be open to browsing, but to comment, you needed to be invited by another member with x karma? You could quantify this by requiring 10 karma to comment and 100 to post, and allowing a user to gain x karma by getting an 'invite' from an existing user with 100 karma.
Of course, without data, it's hard to draw conclusions about the fundamental issues.
Some of these people just create an account to make a few contributions on specific threads and then they're gone. Having an invite system would increase the friction in being able to do this.