I find this sort of thing utterly silly. Somehow, according to this reasoning, churches will be more “free” to exercise their call if they don’t have to worry about their tax-exempt status. Well, I guess that might be true if the “freedom” you’re worried about is endorsing or opposing electoral candidates from the pulpit or in an advertisement. Because that’s about the extent of your worries.
It’s a silly claim because it is actually based in an acceptance of the very same hegemonic kind of thinking it purports to be protesting against. What lots of academics (and the Supreme Court, alas) suggest is that churches are tax-exempt, along with most other non-profits, because they work to serve the public good. And, I think, they do that. And it would be unconstitutional to single out churches for taxation and a significant blow to the American volunteer tradition if all non-profits were taxed. (That’s not to say that there aren’t abuses, but abuse doesn’t undermine the principle). But the better way to understand churches’ non-profit status is that it represents the limits of government, that there are certain things the state may not touch. Non-profit status is of a piece with the recently endorsed (sort of) ministerial exception. Since the power to tax is the power to destroy (to quote the Supreme Court), churches are properly given non-profit status because otherwise, they could be taxed to extinction (at least in theory).
Of course, there are limits, just like there are limits on how many people you can have in your church building at any one time (fire codes) or what you can do with children (no sacrifices). Yes, these are limits, but folks should get real: we live in an age of unbelievable freedom, maybe too much freedom (maybe). Tax exempt status is not bearing down upon us and muzzling the gospel.
Civitas Peregrina 
I agree entirely. There’s also a severe naivete in the thought that once government isn’t giving some sort of tax-exempt privilege, the church will somehow gain more freedom to act and be itself. As if to say, “Well, we’re now paying you, so you should give us some more autonomy.”
The tax-exempt status correlates with a respect governing authorities have for other spheres, in this case the church. As the respect goes down, so will any reluctance to interfere with “religion”, particularly if it is associated with retrograde and benighted social views.