This seems like an "avoid the appearance of impropriety" situation. The HN mods don't want it to devolve into a political board, but killing a controversial story about the model YC company would certainly generate accusations of favoritism.
Almost. See: http://i.imgur.com/qymKtS3.png (see http://hnrankings.info/ for actual page)
Interfering with the "community" system is such a slippery slope and we are apparently watching another one of these revealing moments.