That's a misleading summary of the issues and the result. The facts are different - Germany =/= GITMO, and the Germans actually had a legitimate process that was followed - detailed charges and a hearing and a finding. The "hearings" set up for the prisoners at GITMO were a farce. Kangaroo court is a good enough description, and when decided the Executive branch had six years to set up a legitimate process and deliberately failed to do so.
So the core issue was whether we (the Executive branch) effectively terminated prisoners' rights held under our exclusive control, on land we'd continuously occupied without interference from the Cuban government for a century based on the distinction between an indefinite lease and U.S. owned territory. And the court rationally held that we could not - that the executive branch could not operate without any restraints with regard to those prisoners, and so ordered the Executive branch to provide these prisoners with actual rights to challenge their detention, which is a basic human right.
Nothing I said was misleading in the least. I've read Johnson v. Eisentrager, and it directly addressed the central issue in Boumediene--whether an unlawful enemy alien being detained outside sovereign U.S. territory has a right to file a habeas corpus petition in any U.S. court. The answer was no. You are trying to peddle the nonsense that unlawful enemy combatants are entitled to the protections of the Constitution. That helps our enemies spread their propaganda, and it is false. They are not entitled to those protections, nor have they ever been. See Ex Parte Quirin, 317 U.S. 1 (1942). In the Quirin case, a captured Nazi saboteur was electrocuted without ever been indicted by a grand jury or having had a jury trial, even though he was a U.S. citizen! Too G--damned bad, and good riddance. The alien jihadist war criminals at Guanatanamo deserve even less.
The very purpose of accords like the Geneva Conventions was to encourage belligerents to obey the laws of war by protecting only those who did. Combatants who have violated the laws of war--i.e. war criminals--have almost no rights. They may in some cases be executed right on the spot, after only the briefest hearing. During the Battle of the Bulge, for example, the U.S. Army captured a number of Germans who spoke English, wore American uniforms, and had gone behind U.S. lines to commit sabotage. They were taken to the nearest captain or lieutenant who could be found, and when they couldn't sell their stories, they were taken aside and shot. The Army even documented these executions, which were entirely legitimate, on film.
It is your statement of what was before the Court in Boumediene that is misleading, as is your statement of its holding. No one had even suggested that the U.S. could "operate without any restraints with regard to" the detainees. Although the detainees were unlawful combatants and not legitimate prisoners of war, the laws of war, as Congress has codified them, still imposed certain restraints. The majority cooked up a constitutional right to habeas under the unconvincing argument that a law Congress had passed regarding treatment of the detainees, the Military Commissions Act, violated the Suspension Clause. This was an outrageous, arrogant intrusion by the Supreme Court on both the Legislative and Executive branches in a matter of war, something almost unprecedented in this country's history and itself unconstitutional. President Bush should have ignored it.
In the end, the government complied with the habeas requirement the Court imposed not by giving the detainees access to U.S. courts, but rather through Combatant Status Review Tribunals. These are held at Guantanamo, and the transcripts of at least some have been published. I have read parts of Khalid Sheikh Mohammed's, for example, on the internet. He and the others have gotten far better treatment than they deserved. The bastards should long ago have been marched onto a gallows, had their filthy necks stretched, and their stinking carcases thrown to the sharks. If, that is, a self-respecting shark would eat such rotten stuff.