Before all else, the ISI is essentially Pakistan's DIA, Inter-Services Intelligence. The Afghan Bureau of the ISI came to prominence funnelling several billion dollars from the US and Saudi Arabia to the Afghan mujahideen while the Soviets occupied Afghanistan, and several billion more from Saudi Arabia to the mujas and eventually the Taliban after the Soviets pulled out and US aid was halted.
There is no doubt that the Pak Army and the ISI's Afghan Bureau are still, to an unknown extent, "dirty" and feed intel to our enemies. This is a given and probably explains the use of irregular Pak troops for this operation in its entirety. I would safely assume that ISI's reach even extends, to a more limited extent, to the Pak Tribal Security Corps and the Pak Militia, meaning that the possible implications of your quoted material must include those that you draw.
However, there are also other possibilities that should probably be considered as well.
First off, Nek Mohammad enjoyed immense support from the various tribal clans, the majority thought of him as a hero. In this situation, I believe that he would gain more mobility and safety from this factor than any amount of ISI duplicity, simply because neither the Pak Army, ISI, nor the Pak government has had much influence in these areas until this year and even now, the tribe's jirgas and lashkars seem to favor the militants, paying only the barest minimum lip service to government and militia edicts as is necessary to avoid financial and legal retribution. Indeed, they have been slapped with sanctions numerous times, with little change in attitude.
Additionally, and in part because of the ISI's history of tight bonds with the "enemy", all intelligence is liable to remain tightly compartmented within the military forces active in the region. Very few top officers would be privy to an impending top level enemy meeting to begin with, and they probably wouldn't talk about it with reporters if they were in the loop.
Not looking to argue with you, only to raise additional possibilities. The influence of ISI-Taliban/AQ/militant relationships is indisputable. ISI duplicity in this series of military operations is also highly likely. The main question is the degree and effect of ISI duplicity. If the objective of the Pak military forces is to bring to a halt the militant presence and activity in the border tribal areas, and to either kill, capture, or drive them across the border, then any ISI efforts to oppose these objectives, while possibly significant, have not been even close to a determining factor to date.
probably explains the use of irregular Pak troops for this operation in its entirety.
Independent chain of command to Musharref ?