Toxic replies in threads are even worse than toxic top-level comments. A toxic top-level comment probably will drop to the bottom of the page, and, more importantly, the toxic reply is personalized.
I totally agree here. The replies are the real issue.
Just from personal experience, if I have something to share on the topic, but the discussion already has a couple hundred comments, I look to contribute as a reply to an already highly rated comment. I'm much more likely to get actually engagement that way.
The issue isn't comment quality. It's UI. New comments, even on busy articles, should be discoverable. It should be possible to have discussions past the front-page-life of an article. It should be easy for the reader to decide whether to explore a given thread of conversation in depth or skip it altogether.
