I’m sure that domestic considerations would make them complain about being kept out of the loop even if they were in the loop. They have an issue with the ISI sympathies with the AQ/Taliban, and this threatens their civilian government.
Oh please, it´s more and more obvious that their “civilian government” is a sham. Osama was hiding out in the very heart of the supposedly anti-Islamist Pakistani military. The Pakistani “Deep State” is not on our side, and has never been. We have been scammed - hard.
The Inter-SERVICES Intelligence is not some sort of out of control monster but a wing of the military. The current chief of army staff headed the ISI before he was promoted by Musharraf.