One of the most powerful pressures intimidating Obama was the vocal opposition of seven previous CIA directors, supported by a sympathetic "mainstream" media, to the very thought of holding CIA officials accountable for torture and other abuses. Although it has been long since forgotten, Obama and Holder initially gave some lip service to the concept of no one being above the law.
Unable to prevent Holder from starting an investigation of torture and other war crimes implicating CIA officials past and present, some of those same CIA officials, together with what in intelligence circles are called "agents of influence" in the media, pulled out all the stops to quash the Department of Justice's preliminary investigation.
In a bizarre twist, seven CIA directors -- including three who were themselves implicated in planning and conducting torture and other abuses -- wrote to the President in September 2009, asking him to call off Holder. The letter and the motivation behind it could not have been more transparent or inappropriate, in my judgment.
Afraid of the CIA?
In these circumstances, Obama refused to honor his Constitutional duty to "take care that the laws be faithfully executed." For the same reason -- fear -- he kept on duty the CIA managers, lawyers and operatives implementing the kidnapping, torture, secret prisons and other abuses of the Bush/Cheney years.
The CIA director in place before Obama took office, Michael Hayden, made the mistake of threatening Obama, none to subtly, that there would be insubordination in the ranks, were he to allow CIA officials to be held accountable for war crimes and other abuses. So Obama dispatched Hayden unceremoniously, replacing him with a much more politically astute, malleable, well-connected politician/lawyer named Leon Panetta as CIA director.
Panetta at once took on the function of defense lawyer for the CIA. Virtually all those responsible for the abuses of the Bush/Cheney-era continued in place. And to this day, those operations officers loudly sing Panetta's praise for protecting them.
The only CIA manager who paid something of a price for his open advocacy of "extraordinary rendition" (aka kidnapping and sending captives abroad for torture) and other abuses was John Brennan, one of former CIA director George Tenet's closest lieutenants.
Brennan Too Tainted
Obama had appointed Brennan to lead his advance team at the CIA and it became quickly clear that, initially, Brennan was in line to become CIA Director. But the Senate Intelligence Committee had the book on Brennan, and warned Obama's staffers of the likelihood of a Donnybrook at any confirmation hearings, were Obama to nominate Brennan to become CIA director.
The Senate Intelligence Committee has spent the last three years researching the CIA's detention and interrogation program, in which Brennan played a key role, and reportedly has completed its report. According to a reliable source with good access, Brennan is shown to be one of the senior officials complicit in the worst abuses and that, partly for this reason, the Senate committee will not make the report public until after the November election.
That Brennan had a very soft landing within the Obama administration speaks volumes. Apparently, Obama felt it not quite possible to just let him go, since Brennan knew where a lot of the bodies were buried, so to speak, and would be less dangerous (and maybe even an asset) if kept on the inside.
In any case, whether out of fear of a jilted Brennan or regard for his experience on what Cheney called the "dark side," Obama decided to give Brennan a White House job in which he could still wield considerable influence on intelligence operations without having to go through a contentious confirmation proceeding.
Brennan became deputy national security adviser for counterterrorism, with White House writ over several key functions related to "covert action" -- like compiling lists of terrorism "suspects," including American citizens, to be summarily assassinated -- and CIA-led drone operations.
A Congenital Structural Fault in CIA
It was an unfortunate accident of history that, after World War II, covert action operatives were given a home in a CIA created by President Harry Truman for a completely different purpose -- to give him prompt, no-holds-barred intelligence analysis and prevent another surprise attack like Pearl Harbor. The State Department's George Kennan, on the other hand, wanted to create a strong capability to checkmate the U.S.S.R. by covert action, including overthrowing governments (known today as "regime change").