This seems to be an issue in every online community, whether news-oriented or not.
I'd like to try an experiment with a less open online geek news community. Social trust-based. Very hard to get an account that can write comments. Must be invited or voted to have that privilege. Very easy to get perma-banned. Though, to avoid appearing as Skull and Bones or some other private club, all comments would still be public. Even as a lurker, the insightful comments are often the most valuable thing on a site like this.
There are successful examples of these communities as simply forums in other fields like video game programming, cars, medicine. I'm a member of one for video game developers and one for car computer tuning. There ought to be a good way to apply it to peer-voted news.