A regular complaint of some atheists is that churches pay no taxes. Some go further and argue that this a violation of the Establishment Clause (in that, by granting churches a tax exemption the state is establishing a church). However, this has also come to bite the churches because the IRS will be sent after the church if ever the church appears to be pushing a specific political agenda (endorsing a particular candidate or ballot proposition).
So, one solution might be to determine what taxes SHOULD a church be paying.
FICA, Social Security, etc. for employees - to my knowledge they already pay these.
Property Taxes - this is determined by the State, County and City I assume. What taxes does Goodwill pay for their stores? What does a private school pay in property taxes? What category of owner should a church fall into when determining their tax rate?
Income Taxes - Most churches are non-profits, and their cash flows out as fast as it flows in. I am not sure if they would pay much in income tax, though their accounting fees will probably rise to comply.
So - what taxes should a church pay, and do we structure it to keep it from
A) Being an impediment to worship (removing a tax break on churches WOULD force many to close their doors and would be seen as an attack on 1st Amendment Rights)
B) Sufficient that the IRS no longer has the power to kill a church if the Minister lets his opinions be known in regards to a particular political issue.