Regarding the claim that article [1] was flagged off the front page: It currently has 78 upvotes and 101 comments. As I have explained before‡, articles that have more comments than upvotes and more than 40 comments are automatically penalized by the controversy filter. Thus, it is likely that the article dropped off the front page due to the ranking algorithm, not due to a deliberate effort to suppress the article.
I'm aware of the algorithm. But that story, like the other one, did drop off the front page due to deliberate flagging. Most of the comments came later because the item was shared outside HN (I know because I was closely following it). One of the flaggers was brave and honest enough to own up to it, tried to explain himself, and then was open minded enough or civil enough to be convinced.
It reached around #8 on the front page with about 60 votes and no more than 30 comments, and then, poof, was gone in a few seconds.
‡ http://www.righto.com/2013/11/how-hacker-news-ranking-really...