To begin, a short and incomplete (both by choice and by obligation) discussion of the "prisoner mistreatment" issues, both at Gitmo and elsewhere: There are officers involved who have forgotten their oath of commissioning. It doesn't say "I will be loyal to the political preferences of the President, regardless of their legality or the consequences." It says "I will protect and defend the Constitution of the United States against all enemies, foreign and domestic; and obey the orders of the President and the officers appointed over me." (The exact wording and punctuation have changed over the years, but the substance has been the same since World War I.) Note that protecting the Constitution comes first, and obeying orders is an afterthought. Well, not precisely an "afterthought"—but considering that such a natural military imperative is mentioned only after stating the objective of service should give a hint.
The real problem is the military personnel system. Particularly in deployed and field units, objecting to orders as unlawful—even when they clearly are—will absolutely, positively kill one's career, and quite probably result in immediate adverse action. We have done a poor job teaching officers how to dissent without disrupting the chain of command, both from the standpoint of those who feel a need to dissent and from the standpoint of those giving orders who don't allow an adequate opportunity and forum for expressing that dissent. The "right way" to do it is behind closed doors, with officers only. That can be awfully hard to do in the field, but far from impossible, The problem is that the "experience-based" military culture has come to believe that good ideas do not come from below, unless they are coming from a "fast-burning" subordinate on the way to flag rank. The military academies bear a lot of the blame for this; but the personnel bureaucracy bears even more. I've seen too many stupid and/or incompetent senior officers promoted almost solely based upon groupthink.
The bottom line is simple: Military personnel are people too. Obedience to orders cannot be blind; that way lies My Lai, the Tonkin Gulf Resolution, and many even darker chapters in the history of military careerism. The personnel system, however, persists in refusing to acknowledge this. Those who rock the boat are forever damned—and, unlike private industry, there isn't another employer to whom one can go for a "fresh start."
More-interesting material will have to wait for later in the day.