At the gym the other day, I saw on the TV that Lindsey Graham was complaining about prosecution of terror suspects in civilian courts. I reckon it's up to the executive to decide whether to use the criminal justice system in particular cases rather than some questionably constitutional military tribunal or even more questionable detention without any kind of a hearing. In the absence of some really compelling reason to forego the criminal justice system, I reckon it would make no sense to do so other then to appease some yahoos in the GOP.
I have heard it argued that terror suspects don't "deserve" constitutional rights. This argument doesn't signify. It ain't about deservin'. We all get constitutional rights whether we deserve them or not. Hell, even imaginary people like corporations get them.
I have also heard it argued that affording terror suspects the rights of accused persons in the criminal justice system makes it harder to get them to cooperate in fighting terrorists. I'm not sure why this would be true as a blanket proposition. The potential terrors of the penal system are a pretty good inducement to cooperation. The government won't be able to torture them or to use the fruits of torture, but that doesn't usually turn up anything useful anyway. If you need a false confession, torture. If you want reliable information and leads, don't.