While “tax the churches” seems to be a reflexive sentiment in some corners of social media whenever religious public policy debates take place, I think you’ve explained why that’s not a good idea in the US at least.
Here, we don’t tax any not-for-profit organizations. Singling churches out for different treatment would not only violate our Constitution but our commonly held values. We would be moving from neutrality with respect to religious organizations to hostility toward religious organizations.
That’s clearly not going to happen. Public sentiment would see to that.
But we could tweak things a little by putting churches into the same non-tax paying boat as non-profits like community clubs, charities, and so forth. Require more thorough financial reporting, etc.
That would have the effect of getting rid of the “no political speech requirement,” but that’s only observed in the breach anyway.