Some other portions of Hersh's story just don't seem plausible to me (the Vox piece made a number of these points and more, but personally I think these are the strongest). If Bin Laden was under ISI control, I don't understand why the Pakistanis would have wanted the US to send in SEALs to kill him in Abottabad when they could have just put him on a helicopter and had the SEALs kill him in Afghanistan. That would have avoided all sorts of embarrassment to the Pakistani military and intelligence services. The fact that the US penetrated Pakistani air defenses was very embarrassing to the Pakistani military, as was the fact that Bin Laden was living practically down the street from a Pakistani military academy - not to mention that it seems strange that the Pakistanis and Americans would have chosen to undertake all the risks of discovery of sending helicopters in to a peaceful town when the ISI, which was supposedly guarding Bin Laden, could have just quietly taken him to a remote area.
The business about SEALs dumping parts of his body out of a helicopter also seems strange - given how politically charged the mission was I would imagine that they would have been incredibly disciplined and professional. And Hersh's explanation for the breach in US/Pakistani relations following the mission just seems convoluted and implausible. It seems very plausible to me that the US went in and killed Bin Laden without Pakistani knowledge, and that the mission caused the breach. Hersh's explanation just seems like he's building up a whole convoluted series of explanations to justify his theory.