1) The only case law he cites involves a university not the church itself.
2) The issue he's writing about (gay marriage) may mean that church officiants must sign marriage certificates for everybody or nobody. They can't pick and choose who they sign for. However, the church can refuse to recognize gay marriages if they want to and the government can not, under the Constitution, tell them otherwise.
The constitution is clear that the government can not dictate what a church does within its walls, nor can it favor one church over another. In order to revoke the tax exempt status of the WTBS the IRS would have to revoke that status for all churches. In order to do that it probably would have to revoke it for all non-profits, otherwise its treated churches differently, which it can't do. See the 14th Amendment.