How is easy.... you do it just like other businesses.   You remove the exemption that churches currently have.

Why.... or should you ......  those are entirely different questions.

Here is a thought.... currently, churches are NOT supposed to be involved in politics.  In return for that tax exempt status.  It seems some church leaders tend to walk up to that line... and maybe cross over. If you remove that tax exempt status, then churches and church leaders would be free to be involved in political debate, and political persuasion. 

I am not saying this should be done. You asked the question "why". I am saying this is one reason why