The ally in Pakistan is the government. Evidently our enemies agree: Islamist air force officers tried to stage a coup recently, while Musharraf was visiting the US.
The problem is that there are elements in the Pakistani intelligence services and armed forces that are on the other side, and the government's writ doesn't run throughout its nominal territory.
The Sunni tribesmen in Waziristan are definitely on the other side, but I've not heard of any terrorism perpetrated by Shi'ite 'seveners' (a.k.a. Ismaelis) who make up the bulk of Pakistan's professional class (well not at least since the Mongols got done dealing with them, way back when).
"The problem is that there are elements in the Pakistani intelligence services and armed forces that are on the other side, and the government's writ doesn't run throughout its nominal territory."
Same in our State Department, CIA etc.