There are three ways laws come into being. The categories are:
1) Legislative Law - Enacted by congress
2) Executive Law - Executive Orders and rulings by executive branch departments (this is where the ATF comes in)
3) Judicial Law - Rulings handed down by the court system
All of these become law when they are executed. They are not just opinions. They are, of course, subject to review. The courts can nullify or modify legislative and executive rulings. The Legislature can enact laws that countermand executive or judicial findings.
I agree that the West Virginia v. EPA SCOTUS ruling is likely to rein in some of the bureaucratic excesses that have occurred in the past, but we'll have to wait and see to learn just what effect that will really have.