Those taking the word of the CIA as 'Gospel' need to remember that it is an intelligence agency of the United States set up to further the interests of the United States, not some charitable, neutral NGO trying to present an objective and fair analysis of world affairs.
To project, protect and further US interests is all the agency stands for, and at the moment, given the frustration within the US military establishment at the refusal of the GoP to be proactive, and the refusal of the military to take a front seat (rightly so, it is not its job to be determining which policy to follow), the interests of the US stand in getting the GoP to do what it wants in FATA.
And therefore we are starting to see this concerted drive to shift blame onto a secondary 'state within a state' actor.
The goals are clear, pressure the GoP to take action where it has so far been unwilling to, and in that respect the motivation behind these series of articles and 'revelations' is far from clean.