In nazi germany in order to do what they did to the Jews and other “undesirables” they passed laws, because to make it legal was to make it lawful, or so they thought.
In this case, the 501c3 is the legal handle by which the government can use to after churches, ministeries, church colleges, etc. Remove the 501c3 and you at least remove that handle.
I'm not really disagreeing with your point. I'm just making the further point that, totalitarians being who and what they are, there will always be another handle. The problem isn't the handle, its the Godless totalitarian.
They are not just using IRS rules, they are using zoning rules, they are going after custody of peoples' children. Whatever it takes. So, while I understand that you may consider it good to remove a handle, just know they're coming anyway.