Wow, that was way more in depth than I was expecting. You bring up a very good point that shutting down for a time period might eliminate the trolls of the now, but there will be more people to replace them should the comments open back up. This part I don't necessarily agree with. It's true a lot of the time, but I know a few people that are genuinely trolls in real life, and a lot of what they do and how they act is based on getting reactions out of other people. Needless to say, they aren't the type of people that I enjoy being around. For the most part though, you are right. Hubski does do a great job doing that. thenewgreen is a huge part of it, but I think we all play a role in it. Almost every new member that I've seen who has submitted a post or made a comment has been engaged by somebody in a meaningful way. It's those interactions that provide for a welcoming environment, and cemented my decision to regularly use this site after joining last year. The ignore feature is one of the best features of Hubski. It has the potential to be abused, but its use in dealing with trolls and certain tags is beyond wonderful. It makes it much easier to take away negative users audience, which in turn takes away the point of it for many people.The thing that we often forget is trolls aren't a person.
So, to answer your question, no. I think the issue with Popular Science is a reflection of the broken online commenting system. Stopping and starting up may help for a day, a week, a month. But trolls will always be around and ignorance will always find a way to penetrate through the intelligent discourse. All you can hope for is a strong base of intelligent people who want to stand above the fray and ignore those users who choose to act that way.