Maybe that's a hint that links from such sites aren't mostly welcome here?
I think there's something in this. Constant complaint discussions are a way of applying social pressure.
If every discussion on an article with an egregious anti-pattern gets hijacked, people might tend to submit such articles less, or find alternate sources that don't have those anti-patterns. This costs page views for the sites that do them, and rewards the sites that don't.
Firstly, the way to show what sites you approve of is with votes, not by hijacking comment. Degrading HN comment pages doesn't apply social pressure to anyone.
Secondly, I doubt there's a site on the internet that doesn't have some technical or design issue that someone finds egregious. If everyone did what you're suggesting then every comment thread on HN would get hijacked.
Sure, annoying things are annoying, but maybe the site has their reasons, but maybe those reasons are misguided, but then again maybe not, etc. That's all a great discussion to have, but let's have it in the comments on an article that's actually about such issues.