Intelligence Agencies operate in a Legal Grey area. They use evidence which will not stand up in court (called intelligence) in a similar way to the police forces with whom they operate. There is a delicate balancing act to be achieved: Do you let your fox run, and hope to secure enough to prosecute or do you move in early and prevent an atrocity, but probably let him off scott-free? The latter option must often be taken, and that leads to the temptation to use extrajudicial means to get the man as well. Cover-ups must be pretty easy for people for whom secrecy is their trade.
For most of the UK's struggle with Irish Terrorism, any attempt to step outside the rule of law was counter productive, as demonstrated by the police fix-ups, internment and over reactions like "Bloody Sunday". The rule of law has won, and the terrorists have abandoned the armalite and have focussed their efforts on (organised crime and) the ballot box. This is a victory for doing things by the book.
Many argue that the Islamofacists of Al-Quaeda and the like are different, that they represent a bigger threat than previous generations of bearded nutters. They're wrong. Even 9/11 posed no existential threat to the western way of life. A bomb every now and again is a small price to pay for the knowlege that your govenment always obeys the rules. Let's face it, no terrorist threat represents a greater risk of killing you than driving a car every day, so let's get the risk to the individual in perspective.
So the US government should come clean about whether it lifts people and moves them round the world to places where the security aparatus is not so squeamish about roughing people up a bit. We aren't going to win this war against the fundamentalists until the Arab world stops torturing its own people, and we should stop turning a blind eye to their malpractice. If agencies are complicit then they are accesories to torture. And we don't torture; after all that's one of the reasons for knocking Saddam's regime on the head in the first place.
The CIA should focus on its role as an intelligence gatherer. If it tries to be a global anti-terrorist police force operating in the shadows without judicial oversight, then the potential propaganda coup it delivers to the United States' enemies in the Arab World and the International Left renders any short term gains extremely costly. Secondly without good intelligence, the agencies who should be rounding the bad guys up for trial and imprisonment can't get hold of the right individuals. Evidence obtained under torture is suspect anyway.
America should be setting an example. Camp X-ray at Guantanamo has surely served its purpose and its inmates should be given something like a trial or released. The CIA should leave arrests to agencies who operate squarely under the rule of law such as armies abroad and police at home, and Governments should explain to their agents that a long term strategy for winning this fight involves being better people than the terrorists.