Didn't read the article (have to go out right now), but as for the title alone: bad comments are not a system failure. That's like saying trashy novels are a publishing system failure. (Not exactly, but close enough in my book, pun not intended.) System is separate from content. Systems can try to manage content in a wide variety of ways, but the system itself is never the content. If the system gets to the point where it is the content (a'la North Korea), then there is no real content, only propaganda.
The only types of online website systems I can think of that can provide their own content without it being propaganda are online magazines, corporate websites and the like, where the site owners themselves provide all the content.
To regard a facet of free speech and democracy (some people are stupid, some people are dicks) as being a bug that needs to be fixed... sucky analogy.
To put it another way: criminals are not a bug that needs to be fixed. It's the given society's task to adapt to the fact that there are criminals and dicks and stupid people among us.