Not paying attention to the publisher, I've gotta say that I find myself agreeing more often than not. Sometimes, comments do great- but anything above a readership in a couple hundred thousand, and suddenly it all goes to hell.
You'll get a mix of misunderstanding, people inserting their own bias, memetic derailing bullshit, and a whole lot of people who think they're experts, for whatever poor reason they found. This isn't because they're trolls, or horrible people; We all have done it. We all do it. It's being human.
But the problem is, finding the signal in all that noise is just impossible given our current means of filtering. Different outlets have tried different ways of getting people to put more thoughts behind their posts- requiring real names, Facebook accounts, hell, entire companies like Disqus have sprung up for the exact purpose of trying to foster better conversations. And while they all make a decent change, none of them even solve a quarter of the problem.
About the only solution I've ever seen, is heavy-handed moderation. But that opens you up to 'censorship' comments, as we've seen here. Personally, I can't help but feel like maybe it'd be better if real, substantive stories and opinion pieces just didn't have comments; If a person wants to respond, let them go through the effort of making their own blog post, and addressing the author with it on Twitter or in e-mail. It'd certainly lead to more productive conversation. It's partly why I wish there were more intellectually-minded Tumblr accounts, as their format for this is perfect, with reblogging.
This isn't to say comments are all bad, or that they don't serve a purpose. Just that sometimes, all this social doesn't actually produce better content.