So, the Pakistan intelligence types are telling the NY Times and, by extension, the U.S. to how to act in Afghanistan, as the "surge" is likely to push militants into Pakistan. Because Pakistan is still obsessed with an Indian enemy that is not likely to invade anytime soon, it does not have the forces to deal with the internal threat.
Given that the ISI has been apparently linked to the Afghanistan Taliban and have perhaps been out of the control of the democratically selected leaders of Pakistan, we need to take their statements with a grain of salt the size of the Himalayas.
Relations with Pakistan always involve significant tradeoffs, as Pakistani stability is far more important than Afghan stability (the former has nukes and wars with India) but the Pakistanis are far more concerned with their neighbors than with themselves. Pakistan's obsessions with India and Kashmir have proven to be self-destructive in the past and continue to undermine its best interests. There is not a shortage of Pakistani Army troops, but most of them are facing India, which, again, is not going to invade in the near to medium term.
Not surprising then that American diplomats and generals become quite frustrated. So, we should listen to what these ISI folks are telling the American media, but we should also understand that their agenda may not be our agenda.
PS But they are correct in noting that any serious effort in one spot against extremists/militants/whatever you want to call them will just push them elsewhere--to the German sector in Northern Afghanistan, to Somalia, and to other places where they face less opposition.