I think something can be said for not giving churches special tax status but treating them like all other non profits. That would truly be a separation of church and state. But history has shown the dangers in states being able to control religion, especially with preference for one over another, which is usually just a symptom of an even bigger problem - when religions control states.

To avoid this we would have to grant the greatest right of freedom of expression and right to belief such that the state could not interfere in them. Such freedom is the professed aim of a liberal state. But this might mean that an organization has to be free to organize and express itself through collective action which would inevitably mean that speech is money. It might also mean that religions could participate in pursuit of state.
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Thus the bargain struck that they would stay in separate worlds. This was struck back in the 1700's. Is it time to revisit this given our new experience and how it has played out?

I think this is a worthy topic.