The week our Cruise Missiles missed Bin Laden in Afghanistan, Cohen and Clinton went on MTP and stated that no one knew of our attempt to take out Bin Laden and it was an entire stealth mission. Remember, Pakistan and India were fighting at the time and if we hadn’t warned them of the impending attack, Pakistan would have thought the missiles were from India and a war would have been the consequence. Cohen lied on MTP and several news outlets because they had told Pakistan and subsequently Pakistan had warned Bin Laden. I even called my Senator about this.
I seriously doubt that the Pakistanis could have done much about cruise missiles or even reliably detected them. There would have been scattered reports of low flying aircraft, followed by a loud BOOM in Kabul. They might suspect, they would surely accuse everyone, but they would have been as in the dark as anyone.