“Trust us, this guy is a criminal but we can’t tell you why or how” is not an convincing argument, particularly when it’s coming from people and institutions who are constantly caught lying.
Prosecuting cases that depend on classified national security material is nothing new really when it comes to the federal courts. There is a system in place to do so. The military tribunals are an entirely different beast, although some might say different sides of the same coin. I'm inclined to go with the latter, although I don't think the federal courts are quite as bad as the military tribunals in terms of fairness to defendants.
Handling classified information is something the federal courts are set up for already and do as needed. Its not a novel issue that excuses indefinite detention without trial.