So, for example, if Congress says the military can require the entire domestic population to be Catholic and kill anyone who isn't... ?
That's not how it works.
Congress cannot do anything the Supreme Court says they cannot do
It actually is, and this is why there are separate judicial, executive and legislative branches to put those checks and balances on each other instead.
Congress can do that, can't it? Why can't it? It could declare all competing religions as terrorist organisations.
Obviously it'd be immoral, unorthadox and impractical but I expect Congress has a long history of promoting and stamping out ideologies and they can do it. What little I know about the civil rights era springs to mind.