You have this one precisely on its head. It is the Supreme Court in Hamdan that grants Al Qaeda the status of a nation, not conservaties offended by the decision.
You'll have to be more specific at how this is the case.
I know of no prisoner for whom it is claimed the prisoner was detained in a nation called "Al Qaeda". Some in Afghanistan, some in Iraq, others in various nations. We shouldn't confuse ourselves regarding what is happening.
The US has been detaining people captured in various nations, most of them not wearing a military uniform, many not acting under the direct control of the government of the nation in which they have been detained.
I see no indications that Congress is without the power to enact rules which will cause the trials of these people to proceed exactly as Bush would have them proceed. The difference will be that Congress will have to be explicit regarding the process.
Am I mistaken here? Is there some judicial outcome that cannot be accomplished with Congress dictating how this shall be done?