The primary thing to be looking at is that the courts grant warrants, as they did in the cases you mentioned.
What you are missing is that a warrant for something un-Constitutional is invalid even if issued in accordance with unanimous decisions from the SCOTUS., therefor actions taken to execute said warrant are illegal and are criminal acts carried out under color of law. Dred Scott comes to mind, though hardly the only example of the SCOTUS ruling contrary to letter and/or intent of the Constitution.
Courts are not the final arbiters. People are. What can the government do if most of the population (including a large percentage of workers within said government and members of the military) refuses to comply?
There are already laws on the books regarding citizen rights & responsibilities pertaining to dealing with agents of the government committing criminal acts under color of law. I would refer you there.