I have not flagged it, so I am speculating. But users flagging stories is the most common reason stories with a lot of points leave the front page.
These types of stories tend to get user flags for two reasons: they are more voyeaurism than news, and the actual discussions often become flame wars. Also note that I am not a mod, I've just been here for a while.
There was some talk about them not being appropriate for HN, because it was all hearsay within a fairly tightly-knit group. However, none of them were flagged, as far as I know. I don't know what flagging means on HN - this post is marked as flagged and I had to search for it to find it(I was planning on posting the same thing).
Were the ones that spread suspicion about Appelbaum flagged too? It looks to me as this would be quite relevant news.