However, by focusing on "due process" rather than invoking the First Amendment, he laid out a roadmap for a workaround. That's why the Administration isn't complaining. All they need to do is publish and post rules, rather than having them informally understood, and the problem is solved. Of course, if the Judge then starts applying a heightened scrutiny to those rules or the process for booting someone, that's a different issue. But that hasn't yet happened.
This case could have been much worse. If the judge had decided to ground his case in the First Amendment, that would have been a whole new level of headaches, and there may not have been a workaround at all.