Extremism and Islamic militancy have traditonally been the strong fort and strategic asset of Pakistan's security and intelligence establishment. If Baitullah Mahsood or other war lords in FATA were really enemy agents, Pakistani establishment would've long ago eliminated them like they did in the case of Akbar Bugti.
Further, why is there militancy in FATA and NWFP and why isn't it there in Pashtun areas of Baluchistan?