Your take is intriguing, and definitely worthy of thought, but what I'm not understanding is why freedom of speech is extended to the state and level, and freedom from religion is not.
I guess I haven't been understanding your term "freedom from religion" in the same way you understand it. As I'm sure you know, the 1st amendment doesn't specifically mention a "freedom from religion" in those exact words, but it does protect the freedom to practice one's religion of choice, or not to practice religion at all.
If that's what you meant, then I agree that there is a 1st Amendment right to "freedom from religion" as you put it. And if that right is protected from Congress by the 1st Amendment, according to incorporation doctrine the 14th Amendment also protects it from state and local government. But, if you meant something like the mythical "wall of separation" between religion and government that the anti-Christian MSM constantly bandies about, I don't believe the authors intended the establishment clause to erect any such structure. Jefferson's meaning of that phrase was almost the exact opposite of what the liberal courts have said he meant. The letter he wrote containing that phrase was meant to reassure a worried Baptist congregation that the Constitution protected their religious beliefs and practices from government intrusion, not the other way around.
In any case, it's just an academic fine point anyway. Because in reality any law enacted by any government body at any level that required the practice of or assent to any religious system or belief would be dead on arrival at any court in the land, and rightly so.