"funding militant organizations" isn't the same as committing acts of terrorism. Nobody would have said the US should have responded to the 9/11 attacks with airstrikes on the CIA headquarters.
We are not talking about re-targeting of training and weapons from Afghanistan to Manhattan, but direct planning of an attack with ability to restrain and release the groups on demand. Contra the truthers, even the CIA wouldn't go that far. Musharraf explicitly mentioned the groups operating in Kashmir. He wasn't talking about fighters in Afghanistan.
The CIA wouldn't go that far? Operation Northwoods [1] is obvious evidence to the contrary. The one and only reason that that operation wasn't carried out is because of a President who refused to sign on to it, who would shortly thereafter be assassinated by a 'deluded gunman.' [2]