Someone I was listening to a little while ago (can't remember who or where) was saying that the alternative court would probably be the US' military courts martial. The reason given being that if there was classified information that would need to come out during the trial, the courts martial would be set up to handle that, while the rights of the accused would be the same as that enjoyed by our own military members. I guess if there is a situation where there really is classified information that could cause real problems (and not just make someone in our military or government look bad), that might be a reasonable way to handle it.
Personally, I think we should be releasing all of the people in Guantanamo with an apology and some form of compensation for the harm we have done.