The Establishment Clause
The Establishment Clause wasn't used to interpret a state's laws until 1963, and even then the ruling was based on the "due process" clause of the 14th Amendment.
The Supreme Court has been smacking states over the head for Federal Constitution violations since 1810. Just not religion.
It more or less depends on when people sue for or against specific things. People were not willing to sue over religion until we more or less ran out of places to move away to.
Contrary to public perception, the people who got prayer thrown out of the classroom were not atheists. They were Unitarians, a group whose theological outlook was shared by Joseph Priestley and... Thomas Jefferson.