The problem is in the laws on the books, not with the courts' decisions. Under the law at the time of the transgressions, a non-uniformed enemy combatant literally has zero rights under either international law, nor the Constitution.
The courts cannot rightfully do anything except uphold the laws that are on the books. They cannot make law, nor punish anyone under laws that do not exist. Not even someone who rightfully deserves to be punished. Nor can they prosecute under laws written after the transgressions - that would be, of course, ex post facto.
We need to write laws that protect people from the types of activities that took place under Rumsfeld and his inhuman cronies - laws that cover both civilian and military situations. IMO, all enemy combatants should be held under the international agreements governing prisoners of war. The definitions of military conflict have changed since the law limited Geneva protections to uniformed combatants.
I do not believe they deserve constitutional protections because an enemy combatant is not a criminal - they are functionally a military enemy.
I also believe that we need to write some solid code, both in civilian law and in military law, that prescribes a proper and thorough process for how a detainee is determined to be an enemy combatant. If they are foreigners captured on foreign soil, there needs to be a standardized process to determine their status quickly and efficiently. Anyone determined to be an enemy combatant becomes a POW and is treated as such including all international protections against abuse, torture, extensive questioning, etc. If the process finds them to be a non-combatant civilian, then they should be freed as soon as possible after that determination is made. They definitely should not be held and transported to a major detention facility away from their homes until AFTER they are officially determined to be an enemy combatant.
Foreign persons caught in acts of terrorism on U.S. soil fall under the 14th Amendment, being technically "U.S. persons". But, rather than giving them a U.S. citizen's trial in full blown glory, I would propose we use due process to strip them of any constitutional rights (an act which the 14th Amendment does provide for) and hand them over to military tribunal as rapidly as is possible. ie: if the are not U.S. citizens, and are engaged in acts of terrorism, conspiracy to commit acts of terrorism, or involved in espionage for terrorists or acknowledged enemies of the United States (all of which need to be carefully and specifically defined in our law code), then the due process (trial) should be limited to determine the fact that their actions constitute terrorist or domestic enemy activities, and thereby legally and constitutionally place them in the role of enemy espionage agent. (which holds a different definition from enemy combatant. Enemy espionage agents - spies - can be summarily executed through military tribunal.)
If whatever crime was committed is found to NOT fall under the definition of terrorist or enemy espionage, then the suspect is remanded back to the normal criminal courts and so treated as a normal criminal suspect.