I know a guy who I am assuming (subjectively determining) holds the same beliefs as you do: that the separation of church and state was meant to protect churches and religion from the influence of secular government.

This is the same guy who believes that if evolution is true, we should be able to witness in the world half-cat half-dogs, and half-parrots half-iguanas.

While Beliefs and religions are something we feel in our heart, and generally correlate with our personal tastes, science is something that can be reproduced.

Since government is a consecutive and temporal relation of events, opinions, perceptions, emotions, and charismatic declarations, it isn't really science, in the same way that believing in a Creator or a Savior isn't science.

However, if government is an amalgamation of beliefs and tastes, to provide structure to multiple faiths, or lack there of, and religion is an amalgamation of a more refined set of faith- a logical heirarchy is constructed: government would supercede religion, but only in the way a river supercedes a delta, with neither more subjectively important than the other, but both flowing into the ocean of reality.

Where the water goes when it evaporates is observable, subject to both theory and inference. Until we ourselves are the water particle, we can't submit to know for certain whether we will become a cloud or a bit of dew on a leaf.