I knew someone would tell me if I asked.
I don't know personally anyone who works there, but I don't have any reason to doubt your word that prisoners there are being treated humanely and have been for the last few years.
There's actually a few Pentagon reports on this (the most recent commissioned by Obama). There's a Red Cross office on base, too, to monitor prisoner treatment. The reports said attacks on guards are pretty commonplace, too.
Nonetheless, I'm doubtful if in the past the rule of law was followed as strictly as you suggest before the Supreme Court ruling in 2006 that struck down Bush's assertion that "enemy combatants" were not entitled to protection under the Geneva Convention(otherwise, why make the assertion?) The days immediately following 9/11 were marked by a panic-mode that demanded answers at any cost, and forgive me if I'm not completely convinced there were no beatings or torture other than what has been publicly acknowledged. However I'm open to reasonable discourse on the subject. I'd like to believe the best about the men and women involved in this operation.
I'm not a fan of torture - whether it was institutionally sanctioned (the three waterboarding cases I am discussing) or not (Abu Ghraib). The Geneva Convention rights is a tricky issue. One of my professors at college (a retired Brigadier, was in the JAG corps, etc) was one of the military people who petitioned Bush saying the detainees should at least have the *hearings* to decide whether they are POWs or illegal combatants - something the article you linked touches on.
I'm assuming there was most likely "other things" we are not admitting to but I find it odd the CIA would admit to waterboarding three guys and not anyone else. I don't think it's as widespread and prominent as some commentators are suggesting, though.
From my (albeit somewhat shaky) knowledge of international law presented to me by the aforementioned professor and other people in the field the people we've captured who are terrorists (as in, NOT Taliban from the 2001 invasion) would be treated somewhat similar to Pirates. They're violating the laws of war and thus do NOT have a great deal of protections that soldiers or civilians have under the conventions/other agreements. Things like access to mail, etc are forbidden to these people.
This is a good article by Lawrence Wilkerson(former chief of staff to Sec. Colin Powell ) on the botched methodology of it all:
Some Truths About Gauntanomo
I do accept your premise that trying many of these people will be difficult if not impossible, and that simply repatriating them has its flaws as well. AFA rendition, I also don't like the way the administration is leaving that door open. It's a huge mess to wade through, legally, ethically and morally.
His account is very accurate (especially when it comes to Cheney). But there is something he is ignoring - there's been a good deal of prisoners we've wanted to release but no one is taking them or if we DID release them it'd be to countries where they would immediately be arrested, executed, and tortured - and since we're trying to be nice and upstanding people I think this eventuality would be counter-productive. I don't know what we're going to do with many of these people and I wager neither does the President.
I think we need rendition programs or something similar to go after very specific people. As an aside note, if people think this wouldn't have happened under Gore, here's a quote from Richard Clarke's book (found the quote in Wikipedia but it's accurate):
"... 'extraordinary renditions', were operations to apprehend terrorists abroad, usually without the knowledge of and almost always without public acknowledgment of the host government…. The first time I proposed a snatch, in 1993, the White House Counsel, Lloyd Cutler, demanded a meeting with the President to explain how it violated international law. Clinton had seemed to be siding with Cutler until Al Gore belatedly joined the meeting, having just flown overnight from South Africa. Clinton recapped the arguments on both sides for Gore: "Lloyd says this. Dick says that. Gore laughed and said, 'That's a no-brainer. Of course it's a violation of international law, that's why it's a covert action. The guy is a terrorist. Go grab his ass.'"