The truth is more likely that it’s less to do with his site and more to do with Google seeing a pattern of what it considers to be unnatural linking by the publishers it is contacting. As Haughey guesses, it’s more likely that MetaFilter is “collateral damage,” with the damage being the annoying link removal requests rather than any real distrust of the site. That’s especially since its ranking drop seems to well predate these requests.
But it is worrisome, especially when Haughey writes about how much care apparently goes into trying to ensure all links are relevant:
Earn respect. That’s your best defense if things go south with Google. It’s also your best offense for doing well in Google