The original intent of the BoR was that it applied at all levels of government.
However States were quick to deny that and the early Supreme Court turned away from the original intent.
That's an interesting argument especially considering that immediately after the adoption of the Constitution, a number of the original 13 states enacted state religions.
Where you come down in this debate, I think that it's inarguable that there was contention and controversy with respect to incorporation even in the infancy of the Republic, and not just in the judiciary but in the respective state legislatures as well.