Apparently quite a lot of HNers disagree with you, and liked it well enough to save it. That should be enough to indicate the article is appropriate for hn.

And the low quality of discussion it produced and the number of flagged comments should be enough to indicate that it wasn't. Because people don't just flag for the article, they flag for the thread as well.

Then the comments should be flagged, not the article. There wasn't anything wrong with the article, and apparently it was interesting to the hn crowd - which according to the guidelines is exactly what makes it acceptable.

EDIT: to respond to your edit, there was an entire thread discussing this in the article discussion. The article should be flagged if there's a problem with the article, and comments should be flagged if there's a problem with the comments.