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When you apply for a U.S. passport, the application goes to the State Department for checking. At that point, the CIA has the right to request 30 days to run a check of its own, precisely because of national security and intelligence and, among other things, terrorism.
Would it be okay if they ordered you to maximum security site while they do that? After all, you might be a threat. You might need a medical exam (I hear they do pretty comprehensive strip and cavity searches).
Or would you argue that there was no reason why they should presume in advance that you needed to be incarcerated?
Most of the problems with "countries of origin" have been that the Bush administration was insisting that those countries continue to hold the prisoners without charge. In addition, the U.S. government has kept them on lists of international criminals. Until the U.S. courts absolved the 5 Bosnian-Algerians of all wrongdoing in their habeas petition, Bosnia was unwilling to take them, because they were 'terrorists': so designated by the United States.
As for the "15 or so high value detainees", they got this designation because they were transferred from black sites in 2006. Many, if not all, represent a serious threat to the U.S. in terms of reputation. Two are known to be a real problem: Khalid Sheikh Mohammad and Ramzi bin al Shibh. One is iffy: Abu Zubaydah. Many of the rest were picked up because KSM or AZ mentioned them during torture. Those two have since repudiated their lists, saying many of the people named were just acquaintances or famous families. So we don't even know that all the '15 or so' are even problematic. One is the father of a guy who was sent up in New York state, and is doing 30 years for falsifying an ID (because he was a 'terrorist'). So it isn't even clear that those for whom convictions can be had in court are necessarily dangerous.
When you do things like this that pollute your justice system, and confuse your rolls of criminals, and destroy your normal evidence process, and arrest people on hunches, or because some guy you are waterboarding, after he hasn't had sleep for a while, and was in total sensory deprivation for a month, and whose wife and kids you are also holding and threatening to rape and kill, spewed names and names and names, you don't really have justification even for waiting to find out who you really have. And just because we've all been taught to believe that there are harmless people mixed with hard core down at Guantanamo, doesn't mean that has ever been proven the way real crimes are proven. Hate the U.S.? Quite possibly. In case anyone didn't notice, that is not a crime, or cause for incarceration or military action.