First off, there are no such things as "additional rights". Any of these rights are basic human rights that are not dependent upon any other factor. Likewise, there is no such thing as a person who does not deserve their rights. Such a notion is abhorrent and contradicts the basic values America was based on.
Secondly, I am enraged with the question "What happens if they're acquitted?". The obvious answer is "We let them go." Any other answer is, frankly, unAmerican.
Thirdly, the simple fact that we're trying them doesn't make them criminals. Saying "we've already decided that they're criminals" is absurd; we have made no such decision until we try them.
On the fourth hand, saying that military tribunals have been used since the Revolutionary War is an ad antiquitatem.
Fifth of all, it is absurd to make a distinction between sins (for want of a better word) committed "in uniform" or "out of uniform". The idea of a separate "law of war" is special pleading. Anyways, we should not elevate the actual terrorists by calling this an act of war; this would simply lend them an air of legitimacy.
Of course, I would also like to make the cliché observation that we could free up a lot of space in our prisons by freeing all the nonviolent drug offenders.
On the topic of torture, the idea that the torturers were trying to make us safer doesn't mean they didn't break the law. No, Graham. Using techniques not outlined in the manual does not make it illegal. Using torture, which is against international law, does. Then again, you "saw the law as a nicety we could not afford." But you aren't criminals. Riiiight.
I would like to end with a quote from Blaise Pascal.
Can anything be stupider than that a man has the right to kill me because he lives on the other side of a river and his ruler has a quarrel with mine, though I have not quarreled with him?