According to the Wall Street Journal's Siobahn Gorman, "a secret Central Intelligence Agency initiative terminated by Director Leon Panetta was an attempt to carry out a 2001 presidential authorization to capture or kill al Qaeda operatives, according to former intelligence officials familiar with the matter."
It's a curious story. So Congress knew about the finding (which has been previously reported -- first by Bob Wooward in Bush at War, then elaborated on by Ron Suskind and others) and the revelation is that the CIA had a cell that was still proposing ways to carry out the finding? That doesn't seem objectionable... especially if the finding had been fully briefed to Congress and the CIA hadn't authorized any action operations.
What's ticklish is that the Joint Special Operations Command, operating under the 2002 Authorization for the Use of Military Force (against Al Qaeda) and the Bush/Cheney Article II inherent authority rubric, fairly routinely captured/killed Al Qaeda leaders in places like Yemen and Somalia... without the permission of the country involved. (The CIA often provided intelligence to help these efforts.) The CIA needs a presidential finding to begin a covert op; for a clandestine op (an operation that results in something public but whose originator is hidden), the disclosure requirements are different. And the Bush administration claimed the inherent authority to capture or kill Al Qaeda leaders anywhere under its interpretation of terrorism as a military matter.
One former CIA official who has no direct knowledge of the program told me he had been told that the secret program Panetta discovered involved deceiving countries with which the CIA had developed anti-terrorism liaisons.
So maybe it was a program designed to provide cover for covert ops in friendly countries to capture or kill Al Qaeda leaders operating in areas non-contiguous to the battlefield.
The CIA uses predator drones to kill Al Q leaders in Pakistan, occasionally without direct permission from the Pakistanis, which is technically covered by the AUMF. Without reference to the law, it's a distinction without much of a difference.