I would say we're going to eventually find out two things: the Pakistani government was not in on the takeover (though people may have been bribed to look the other way), and it isn't Al-Qaeda, but either an Iran-backed new Shi'a terrorist group, which would explain the silence, or a Uyghur-backed group, which would explain the China connection.
Why would Iran be complicit in the hijacking of a plane full of citizens from it's main petroleum buyer and major supplier of military technology?