Reading the documents (I'm doing mostly appendixes first) it becomes obvious that what this is really about is a CIA turf war. They are mightily pissed that they were routed around--accurately, legally, or not--and this seems to be a large issue in the documents. Might also explain the current plentiful supply of "anonymous intelligence officials" dropping tomatoes on the administration.

Precisely.

The reality is the CIA is a political body as well as an intelligence agency and Bush chose to use the "backchannel CIA" comprised of, as the media has identified them from time to time,"Special Activities Directorate" folk. This was a good choice because the front end political branch is the most compromised. Double agent horror stories aside, there are enough folks on the front end who simply work for our enemies and it's not just Russia anymore. China, India, France, UK, Germany and others invest heavily in saturating allies intelligence agencies with human assets. And that's not the only problem when trying to conduct operations clandestinely.

The Director of the agency is a political appointee and often is not well acquainted with career CIA folks. The career folks often usurp the Director's power because they know the ins and outs of the organization and channel orders and initiatives to their own 'clique'. Whereas the backchannel folks are largely apolitical. That generally helps a lot when conducting ATS operations.

Bush worked, almost exclusively, with the Director and then straight to the backchannel folks whom the Director could coordinate, bypassing much of the CIA management.

You can find tons of CIA employees who will rant "off the record" against Bush's decisions. Everyone from the stenographers and secretaries to certain strategists at Langely who feel their expertise was not tapped.