Churches need not even file as a 501(c)(3) to be recognized as tax exempt. This is a fallacy and disinformation. A church, as a "religious, non-profit" organization should not be held to suppression of political speech.
I know absolutely nothing about the tax code so I can't discuss the legalities of this with you. Churches are a business, they have investment portfolios, real estate, and power. They want to act like a business, they should be treated like a business.
http://www.freerepublic.com/focus/f-news/1363096/posts
http://www.freerepublic.com/focus/f-news/1349958/posts
http://www.freerepublic.com/focus/f-news/1335649/posts
http://www.freerepublic.com/focus/f-religion/1320563/posts
http://www.freerepublic.com/focus/f-news/1295847/posts
I threw in a couple of posts that I have read that made me realize that churches are as morally corrupt now as they were in the past.