I think it should rank naturally - even if some people would rather it didn't - if it's ranking, then people must want to see it.
IMO, if people are flagging articles to get rid of them, just because they don't like them - rather than just downvoting, then this seems like an abuse of the flagging system and there should be some sort of repercussion (flags/day? lower?)
People are supposed to flag submissions that do not belong here. It's obvious that many of the NSA articles didn't belong here - there was nothing intellectually stimulating about them and they contained no new information. The discussions didn't have any useful advice about protecting your information, or about what to do as a startup if a government agency requested your data, or etc.
There are repercussions for too much flagging - you (so I've been told) lose the ability to flag anything.
You can't downvote submissions (or at least, I can't. If you can it must require a certain karma threshold). So perhaps some see flagging as the only option for expressing disapproval of a given story.
IMO, if people are flagging articles to get rid of them, just because they don't like them - rather than just downvoting, then this seems like an abuse of the flagging system and there should be some sort of repercussion (flags/day? lower?)