I agree with you that this was a bit ranty but this section stood out to me because it captures my thoughts about the PopSci comment shutdown very well:

That seems to be the point—which is to say there really isn’t a point other than that they wanted to shut the comments down because they were annoyed by trolls and spam-bots. The upshot: trolls win. Trolls are just online bullies, with many being very dedicated to shutting down, derailing, or drowning out discussions. PopSci has let the trolls win and has punished its readership as a result.

Perhaps I'm biased but letting the trolls win is a misstep anywhere, especially in a large publication where other people may be encouraged to follow suit. This is also the same reason the HuffPo verified identities worries me. Comment sections may be trash most of the time but I think they are a necessary to promote discussion, transparency and community. Obviously if every comment section was filled with insightful comments Hubski may not be able to exist in it's current capacity. Why would we need outside sites to promote discussion if every site had stellar commenters?

My point is that giving up or placing ridiculous limitations is a step backwards in an age where so many people user online media to become informed on a variety of topics. While having a superb comment section may be tough, so is running a magazine or blog in general.

I haven't fully fleshed my ideas on this topic out completely but there is something remarkable happening with transparency worldwide. We see our government, a government that promised transparency, doing the opposite. We see sites hiding behind vague messages and reasonings in order to "protect themselves" (whatever that means.) We see comment sections disappearing or becoming and exclusive offering. In an age where everything happens instantly and everyone has the ability access to everything, why are we moving backwards in this sense? Shouldn't transparency and community and promotion of great ideas become easier?

Are we so inundated and scared by these old school ideals of what is found your page, your site, your ramblings is an 100% reflection of the publication or the person? Are we scared that our 300 word "article" is going to be covered up or meaning altered by a slew of bad comments?

Perhaps we - everyone, every site - should be focused more on figuring out how to educate internet users on making informed decisions and fact checking things they read online themselves rather than trying to protect them from anything that may be misinterpreted. You can't dumb down the world forever.