There has been considerable debate of late as to whether the incoming Obama administration should prosecute members of the Bush administration who were responsible for violating civil liberties and human rights. In addition to the theoretical arguments that have been offered against such prosecutions, let me offer a practical one based on my experience as criminal defense attorney.
There is almost no possibility that such prosecutions could succeed. A fairly selected jury would almost certainly acquit. The defendant would simply present the jury with the classified intelligence that demonstrated the extraordinary threats facing the United States. If the government refused to declassify these threat assessments, the defendant would have a strong case for dismissing the charges against him, because he was being denied his right to present relevant evidence under the Sixth Amendment. Most jurors would be extremely sympathetic to the Jack Bauer, "Do whatever it takes to stop terrorism" argument.
A defendant in such a case would also invoke Thomas Jefferson who strongly favored breaking the law in extreme cases of national security, Abraham Lincoln, who repeatedly broke the law, and Franklin Roosevelt, who not only broke the law but ordered the racist detention of more than a hundred thousand Japanese-Americans.
An acquittal in such a case would be seen by many as a vindication of the Bush policies, which is certainly not something those who advocate prosecution would welcome. So be careful what you ask for; you may get it.