That's a good thought exercise.
Imagine Congress passed a law that nobody was allowed to own a gun unless they were a registered member of a state-regulated militia. All gunowners who did not meet this standard were to turn over their guns which would then be melted down.
The NRA (and others) would sue, saying that this law violated the 2nd Amendment of the Constitution. They would also likely ask the court to enjoin the enforcement of this law until the constitutionality was resolved.
I think it's more than reasonable for the court to grant that injunction. Confiscating and destroying people's property would cause harm that wouldn't be easily reversed should the law later be found to be unconstitutional. Therefore, preventing the enforcement of the law until the constitutional issue is resolved makes a lot of sense.
Same in the case you provided: there is a suit alleging a provision of the law is unconstitutional (violating the prohibition of bills of attainder as opposed to 2nd Amendment violation) so the court is preventing enforcement of that specific provision until it can address the constitutional issue.
Seems incredibly reasonable to me. Not a deep state thing, just a logical way to work through the issue.