I think the problem is better stated as a large flagging contingent, rather than anything intrinsic to the site's code or official moderation. And the real problem is that it has an outsized chilling effect on substantive comments, which require putting in actual effort just to possibly be killed. From what I've observed comments/stories get a penalty from flags (before they actually end up [dead]) and this seems to be the actual objective - to stymie concrete discussion while a topic is popular.