Create a subreddit for a news site, and each new article on the news site automatically gets a new post on the subreddit. Embed the relevant post on the news site.
Since "karma" is transitive across Reddit and across news sites, users are slightly less likely to troll. You could also do this with some sort of reputation system across websites (Disqus could add in something like that).
The big problem with news sites is that the communities aren't big enough that there are any negative correlations associated with being a dick. Even facebook runs into this problem because there isn't any way to "punish" someone for a rude comment. Transitive, persistent reputation is key to solving this issue (at least in my very non-expert opinion). Reddit helps, with comment karma and post karma... but it obviously isn't perfect.