When government starts intruding on religious freedom, religious people are adamant that church and state remain separate—until they see an opportunity to use the government to further their agenda.
And the statists are adamant that religion should have no influence upon the government—until they see an opportunity to use religious institutions to further their agenda. History has shown this to be a common theme, and our present day institutions are going down the same road.
We need to understand that both religion and government are two parallel lines of effort, both trying to accomplish the same thing: keep humanity from self-destructing.

“But usually, we support the separation of church and state.”
Both lines of effort have an abysmal track record in this regard. In fact, both have an equal success rate of 0%. Not one religion, not one governmental system has ever offered a lasting solution to the human condition.
So while freedom of religion and freedom of conscience are important, let us remember that both religious and governmental institutions will have a tendency to strive to increase their power.
That’s why I seek something that transcends political and religious differences. Something that will provide a more enduring solution. For me, seeking God outside the bounds of religion and seeking the source of virtue outside the bounds of governmental coercion seems to be the only viable approach.
But as long as we pursue systemic solutions to our corrupt human nature, we should not be surprised at the machinations and manipulations of our religious and governmental institutions.