If you submitted an NSA story and it fell off the front page, it was user flags that did it, not the penalty.
"That Daniel Gackle is the HN moderator" is the kind of factual detail you might want to know before developing very strong opinions about how the site is run.
Second, if you don't trust the site moderators, HN isn't going to be a pleasant place to spend time.
The story in question here had 200 upvotes when it was a link to an NSA story at Slate. The link was changed to the same, source NSA story at First Look and it was quickly flagged to oblivion. I think there're likely some monitoring scripts and flag alerts at play, not just NSA fatigue by actual users.
But many articles are flagged by users, don't assume that all the penalties/kills are dew to moderators actions.