From the article:
"John Koskinen, the commissioner of the Internal Revenue Service, told a Senate committee that he would not take the initiative to revoke the nonprofit status of religious colleges that oppose same-sex marriage, but left the door open for such revocations in the future.
“While I greatly appreciate Commissioner Koskinen’s word that he will not target religious institutions for their religious beliefs, it worries me, and it should worry every American, that the IRS does not absolutely disavow the power to target religious institutions based on their religious beliefs, even if the current IRS commissioner has committed not to use that power for the time being,” said Sen. Mike Lee (R-UT). "
I would be more concerned about religous institutions which do not uphold their church teachings through their practices.
I would expect that it would be easier to challenge their credibility and thus their right to a religious institution exemption.
Those institutions which adhere to the magisterium will be able to use this adherence to prove their religous identity as they struggle over these issues in court.