It may have worked well until now, but I worry that in the future it will allow future administrations to threaten tax-exempt status for churches that don't conform their teaching to society's preferences in the moment. Churches shouldn't be in it for the money anyway. We should just rip that entire band-aid off and undo something we never should have done in the first place.
I have a feeling that most people probably don't give $18,000 to their churches annually. At a 10% tithe rate, that's $180,000. Wel above the median household income.
If we subject churches to taxes, then if you church is paying a significant chunk of money to taxes, then your church is not spending the money on charity like it should be.
If your church is spending the money it receives, that spending is deductible. Spend it and you won't pay a tax.
Maybe a "church" should only be allowed to have the amount needed to fund reasonable operating expenses (plus some emergency funds and charitable work).
If you have more you aren't a church, you are now a business and standard business rules and taxation should apply.