As the ACLU says:

Continuing to detain a person indefinitely without charge or trial for a crime for which he has been acquitted is absurd and unconstitutional. If the government has sufficient evidence to warrant criminal charges against prisoners held at Guantánamo, it should file those charges and prosecute the prisoners in ordinary federal courts. But the government should not be holding prisoners indefinitely without charge or trial, and it should certainly not be holding show trials from which guilty verdicts will be honored but acquittals will be ignored. The suggestion that the government can protect the country only by disregarding the Constitution is an extremely dangerous one that should be unequivocally rejected."

The first issue here is the unfairness of the Military Commissions, which cannot be fixed. They must be scrapped. As the ACLU says,

"For the first time ever in a public setting, a Justice Department official testified that the Due Process Clause of the Constitution applies to the military commissions at Guantánamo and, as a result, that coerced evidence must be barred from military commission trials. But it is too late to fix this irreparable system that flies in the face of the most basic principles of our democracy and justice system.

The military commissions system was set up to circumvent the law and the Constitution in order to achieve easy convictions, not to provide justice, and the results of such a sham system will never be legitimate. The only way for America to live up to its highest ideals is for the president to commit to ending the Guantánamo military commissions, trying detainees suspected of a crime in our federal court system, and resettling or repatriating those who are not charged and tried."

We should make no distinction between holding a detainee indefinitely without charges or trial and after acquittal at trial. Indefinite detention in the absence of a conviction is abhorrent to our system of justice.

If there is evidence against someone, charge them in federal court and try them. If the evidence came about through torture and is inadmissible, it is not acceptable for the U.S. to hold those people without charging and trying them because it fears an acquittal without the coerced admissions. The constable blundered, the suspect goes free. It's been that way for 200 years and there's no reason to change it now. In this case, the U.S. can try to repatriate them or send them to another country. If no other country is available, then they must be released here. If the government doesn't like that, then next time it should ensure its agents follow the law and Constitution when interrogating suspects.

What kind of deterrent will it be for torturers if they know there is no need to fear an acquittal because there won't be a trial? All they have to do is give a heads-up to the military, "I don't think you want to charge this one, you won't get a conviction" and his goal is accomplished: No charges will be filed but his victim remains locked up, indefinitely, perhaps for life.

That's too much power to give the military. We need judicial oversight of those charged by Article III judges who are not beholden to the military. And, we need to allow those not charged to file habeas petitions in federal court seeking release.

It's really quite simple: It's either Federal court or release them. If the Government loses in federal court, hopefully they'll learn to conduct their investigation and interrogations legally next time.

Indefinite detenition, either before charges and trial or after trial and acquittal are two sides of the same coin: Both must be rejected.