While I believe the SCOTUS will find on behalf of the church, the big argument will be whether they reach a narrow or broad decision.
Religions are essentially exclusionary, almost by definition. If they were not, they would have no distinct purpose in being.
However, the SCOTUS could also hit a home run by declaring that *secular* and *semi-secular* activities owned and operated by a religion or church may also be exclusionary.
For example, Catholic hospitals could not be required to issue birth control or perform abortions under Obamacare—which in turn would be a stern indicator of the intent of the court when it hears the Obamacare case.
States and the federal government could not force parochial schools to do much of anything, unless it was done voluntarily in exchange for government money, and teachers were otherwise certified.
However, there is also a big problem with school curricula, if it teaches things that are not legal. On one hand Muslim schools could be prevented from calling for murder and the violent overthrow of the American government. But on the opposite tack, government might decide it is illegal to teach that homosexuality is wrong.
So this is going to be a very interesting court case from a lot of angles.
I have a HUGE problem with your analyzes. Nether the Federal Government nor its SCOTUS employees have any business telling Any religious institution to do, or not to do anything nor any school for that matter.
Yes under the same ground Muslims could teach hate and overthrow of the Government. That is intrinsically a right which the Federal goverment is not authorized, indeed is specifically PROHIBITED from usurping.
The States on the other hand are an open book subject only to the limits of their own Constitutions in this matter, as with most every other matter.