My earlier proposal (http://news.ycombinator.com/item?id=2242453 ): deduct karma from submitter and _anyone who upvoted_ on submissions that were successfully flagged. That should get people to think the way you mention not only when submitting, but when upvoting as well.

Improve the submissions and comments will naturally improve -- submissions that are one-sided/gossipy/demagogic tend to attract similar comments. Whereas submissions full of technical content are often rich with links to further reading, contrasting viewpoints with cited evidence, etc. (Disclaimer: observations in this paragraph may be subject to fundamental attribution error).