While it would be unconstitutional to tax churches but not to tax other non-profits, it would be fully constitutional to tax all non-profits equally.
What about the McCulloch v. Maryland precedent?
I think you're reading too much into the
McCulloch decision, which I believe was really only to be applied to the sharing of power between the federal and state governments. Yes, it was said that the power to tax is the power to destroy, but the government taxes other things that it cannot constitutionally "destroy," like the press, which is protected under the First Amendment just like the free exercise of religion.