That's a tough problem. Outside of human moderation I don't have any idea. I'm glad you're aware of the problem though and are working on it. You guys work hard and we pay you nothing!
Thanks. I may write some code to show moderators a view like /newest but only from sites marked lightweight. Then we can rescue any solid articles from the penalty. If we can save most of the solid articles, it would free us to mark more borderline sites as lightweight. An experiment worth trying, anyway.