I don't think this is really about trolls for trolling's sake. I think this is about being called out on sloppy content.
We all know that online journalism is a seriously tough business, especially for anyone trying to maintain some sort of reputation for quality. For these guys, it's economically infeasible to make sure every article is high quality because the headline is <insert very big number here> times more important than the body and there are plenty of competitors taking advantage of that.
So when a site starts publishing empty content because they feel that they have to, comments are rightfully merciless on calling BS. Writers get demoralised and publications look for ways to save face. As pointed out, removing a comments section is far preferable to heavily moderating against unfavourable comments. But still, I hate the trend we're seeing.
The Verge is an interesting one. They selectively open comments but many articles remain closed. It's not entirely clear how they decide which articles to open but there at least seems to be a tendency to open comments on the longform stuff they're proud of.
Longer term, everyone is looking for a model where quality is rewarded or at least some sort of rebalancing for the internet publishing economy. Blendle wrote a nice article about their experience getting consumers to pay: https://medium.com/on-blendle/blendle-a-radical-experiment-w...