How and why is the supremacy clause pertinent? If the Constitution doesn't expressly grant the U.S. legislature authority to establish a national religion or prohibit the establishment of a state religion how can a law pursuant to that constitution have supremacy over a conflicting law from a "subordinate" legislature?
There shouldn't ever be a conflicting law between state governments and the federal government bc only the general government can legislate on items granted to it by the Constitution and only the states can legislate on items not granted to the U.S. government in the Constitution. Those are two distinctly different areas of authority and inherently can't conflict. The only time the supremacy clause should strike down a state is if a state attempts to legislate on an area in which the federal government has been granted authority by that state. Otherwise it's irrelevant. In this case, the federal government has no authority on the matter of religion so the supremacy clause should not apply to the states.
I mean, that's just not true. It might have, but we have amended the law since then, as is the design of a Constitutional system. That is the nature of our system. You can say "Well I disagree with the SCOTUS" or "I disagree with subsequent Amendments" all you like, but that has zero impact on the force of law and the clear interpretation for 150+ years has been the opposite of what you say here. The Civil War fundamentally shifted the role of the federal government in the US, and the amendments made to the US Constitution as well as the Common Law precedent set on those opinions are pretty clear on that matter.
Regarding secession, states most certainly reserved the right to secede during ratification. Virginia most famously reserved the right to secede as a condition of ratification, but a few other skeptical states did too. Virginia would not have ratified (Mason and Henry were winning the argument) had secession not been reserved as a right during ratification. Patrick Henry still didn't support ratification. Rhode Island was another such state. It wasn't until Lincoln that this notion was ever challenged.
This was a debate that went back to the founding of the nation. See Madison's comments on New York's requested condition, and Virginia's claim that you mention. From the founding of the nation there was debate as to whether it was a perpetual union or one that where the states had a right to withdraw if they so desired. It was not settled. While those who try to argue the Confederacy didn't secede over slavery are obviously wrong, it's true that if it wasn't slavery we probably would have ended up fighting a war over some other point of contention leading to secession. After 1865 that matter was settled, and the perpetual union side won out clearly both in force and in common law.
The 14th amendment specifically applied to the freedmen emancipated by the 13th. Initial court decisions agreed with that limited scope. It has since been broadened and broadened again and again to what you accept now. The due process clause is supposed to only ensure all people emancipated by the 13th amendment were treated the same as states treated their citizens prior to emancipation. It did not, nor was it intended to, incorporate the 1st or any other amendment into its umbrella. SCOTUS did that many years later after overturning a prior court precedent.
Should probably be careful with our language here. The 14th Amendment did not 'specifically' apply to freedmen. The word "freedmen" nor "emancipation" is not found in the text of the Amendment at all, certainly not in Section 1 that is the basis for the legal rulings that you might object to. That may be the
context that led to its ratification or the original
intention of the Amendment, but there's a reason that language was used, and there's a reason that text was not limited to former slaves.