This is interesting. Last November, the New York Times revealed a secret Bush administration order that authorized commando incursions into Pakistani territory. President Obama's new Afghanistan commander shows up in the piece:
Former military and intelligence officials said that Lt. Gen. Stanley A. McChrystal, who recently completed his tour as head of the Joint Special Operations Command, had pressed for years to win approval for commando missions into Pakistan. But the missions were frequently rejected because officials in Washington determined that the risks to American troops and the alliance with Pakistan were too great.
Capt. John Kirby, a spokesman for General McChrystal, who is now director of the military's Joint Staff, declined to comment.
We'll see if he favors a similar approach now that he has a higher profile.
Update: Yglesias has a related item about McChrystal favoring CT operations over COIN--though it's far from clear that they're mutually exclusive.