They sided with the church in ensuring that the special religious role of ministry would be protected from government interference.
At the same time, SCOTUS concluded that they "are reluctant, however, to adopt a rigid formula for deciding when an employee qualifies as a minister", but if they are deciding on a case-by-case basis, do you find it reasonable that all associated members would be found to be exceptional (and exempt)? It may be possible for a specific religion. It is certainly not the case for the Catholic church, who have spent centuries defending the legitimacy of their ministry as uniquely empowered.We agree that there is such a ministerial exception. The
members of a religious group put their faith in the hands
of their ministers. Requiring a church to accept or retain
an unwanted minister, or punishing a church for failing to
do so, intrudes upon more than a mere employment deci-
sion. Such action interferes with the internal governance
of the church, depriving the church of control over the
selection of those who will personify its beliefs. By impos-
ing an unwanted minister, the state infringes the Free
Exercise Clause, which protects a religious group’s right to
shape its own faith and mission through its appointments.
edit: Regardless, they did not overturn the existing precedent in which "formally neutral laws of general applicability may regulate religious conduct (along with other conduct) regardless of the adverse or prohibitory effects on religious exercise" in this decision. Employment as a minister is not the same thing as participation in a general and neutral policy program.