One of the reasons the transfer is occurring is the fact that the intelligence value of these detainees no longer warranted keeping them in CIA custody. These detainees were senior planners like Abu Zubaydah, captured in April, 2002 and Khalid Sheikh Mohammed, captured in March 2003. Not only did CIA have a lot of time to get information, but the leadership of al Qaeda has probably made changes in their strategy due to world events.
The CIA system will continue, though. It provided a means to get information that can prevent attacks from happening. Many of those who were held in this secret system were senior members of al Qaeda, and had a lot of operational information. A number of the thwarted attacks were revealed through interrogation of these senior personnel of the terrorist organization. These are the people who planned operations, and also supervised training. They knew who was sent to various countries, and what operations were planned. Their successors will have similar knowledge.
The CIA's ability to use alternative interrogation techniques is another option that is being kept open. The CIA interrogation methods appear to have worked, apparently thwarting attacks (including a plotted anthrax attack). Not much is publicly known about what techniques used by the CIA ultimately broke the prisoners. Barring a leak, you won't hear the details. This will help break future high-level al Qaeda operatives held prisoner, and generate more information that will be used against the terrorist organization.
The Supreme Court ruling in Hamdan v. Rumsfeld, has also opened the door to lawfare against individual Americans. This is because Common Article Three of the Geneva Conventions has very vague wording. That leaves a lot of room for a sudden change in what is legal and what is not legal – simply by virtue of different rulings around the world. Congress has been asked to pass corrective legislation that sets an objective standard that will be declared as compliance with the Geneva Conventions, but until then, there is a risk to American personnel whose only intention would have been trying to stop a terrorist attack. Even then, any legislation may become the target of lawfare from human rights groups that seem more interested in protecting terrorists than in protecting innocent people. – Harold C. Hutchison (email@example.com)
President Bush's recent decision to transfer fourteen high-ranking al Qaeda detainees from CIA custody to the Department of Defense is due to a number of considerations, not the least of which was the Supreme Court ruling (Hamdan v. Rumsfeld) this past June. That decision not only struck down plans for military commissions, it set up a legal minefield for American counter-terrorism efforts.