It’s always tricky when you have to balance competing rights, such as the freedom of a religious group to have it’s beliefs and practices and basic human rights.
It’s not like it hasn’t happened before. The LDS church discriminated against black people until the IRS threatened to remove their tax exempt status in the 1970s. So far there have been no similar threats. The recent cases in places like Illinois and Washington, DC have been for the government to remove financial support to religious charities that discriminate against people based on sexual orientation. A move that is certainly justified, since why should the state give money to a group that discriminates against some of its citizens?
(Via Jesus and Mo)