No but they are still the Court and have a constitutional rule to play.
yes, it does matter who makes up the court. these are the decisions of men, not gods. if we had more Thomas's, the administration wouldn't be forced to do this "end run" as you call it.
Consider this analogy. Let's say police arrest someone for a crime, but don't think they'll be able to get a conviction - are they allowed to simply hold the suspect forever, citing the liberal-bleeding hearts in the judicial system. Even if you disagree with the results, you have to obey the law.
the guy robbing a 7-11 is not an agent of a foreign power. that's the difference. either you accept that there is a difference between the two, or you do not. the US criminal justice system is not designed to prosecute someone like Padilla, given all the rules of evidence and what must be revealed in open court. that's how this whole thing started.