The raging question of the moment is whether it is a good idea to prosecute members of the Bush administration for war crimes, crimes against humanity or just for some simple crime because they condoned the torture of three well known terrorists and in the process discovered and prevented a "second 9/11" attack on the United States.
Some have argued that wrong is wrong and must be punished. Others argue that the ends justify the means. In a nutshell, this is is the eternal conflict between the lesser and greater evil. Is it excusable to do something which is morally wrong if it prevents something much more heinous? One of the perils of being in a position of authority in government is that part of that job is to make the unpleasant decision to occasionally do something immoral in order to prevent a greater evil.
When our leaders do this they run the risk of being held accountable in the judgment of their successors or in the judgment of history. What happens, quite often, is that they are held accountable in the immediate aftermath and then exonerated by the court of history, which tends to be more dispassionate. When Harry Truman authorized the murder of thousands of innocent civilians with the atomic bomb to save the lives of even more soldiers and end World War II, he was not held accountable under the law and the debate over his culpability still rages among historians.
There are many who would like to single out top members of the Bush administration for punishment because they approved the waterboarding of three known terrorists, but the main stumbling block to doing this is that the US did not have a clear law on torture of foreign spies or terrorists and the Geneva Convention does not apply to prisoners who are not identifiable, legitimate military combatants. In fact, the Geneva Convention was specifically worded to exclude spies and saboteurs and terrorists and fifth-columnists from its protections. The US Criminal Code makes the same assumptions as the Geneva Convention about to whom restrictions on torture apply. There's a giant loophole where the Geneva Convention assumes that terrorists will be treated as criminals, not prisoners of war, but where US law and the rights guarantees of the Constitution do not apply to foreign nationals. Ultimately the problem here is not the actions of the Bush administration, which some would like to punish out of spite rather than legal justification in some sort of McCarthyesque witch hunt. The real failure is not having clear and applicable law prohibiting agents of our government from torturing those not protected by the Constitution.