“There have been a couple of Freepers who have tried to highjack the discussion”
I don’t believe they are trying to hijack the discussion. I believe they honestly believe that the 501c3 is a handle that the government can use against them. And I agree with this position.
“I agree that churches should not file, but the fact that they do does not mean that they relinquish their rights as American citizens.”
You must be aware that you have just equated churches with American citizens. A church is not an American citizen. A church is made up of individuals, and in America more than likely American citizens. Your enthymeme syllogism is a fallacy based on the false equivocating of the two subjects. You cannot take a general (churches) and equivocate it to a particular (individual). This will lead to a false conclusion by the incorrect use of the undistributed middle.
A legal entity such as a 501c3 church is bound by certain criteria as defined by the IRS. But individuals, not acting in a representative manner for the 501c3 church, are not bound by the 501c3 IRS criteria.
I am using a figure of speech.
The church is an institution. As an institution, the church-as a body of believers- does not relinquish its freedom to assemble and worship simply because the board of elders/governing body file a 501 c3.