The IRS should simply wield a big stick to prove that churches are using their money for charitable ventures. Churches shouldn't be subsidised for just existing, they need to provide a greater benefit.
There are many non-profit 501(c)(3) organizations that use their money for purposes other than charitable giving (museums, fraternal societies, sports leagues, etc). Again, you're not understanding that the reason religious organizations are tax-exempt isn't because they get a special exemption for being religious, but because they fall under a wider category of institutions (non-profits) that are tax-exempt.