That would be the government getting involved with religion, which is not allowed.
Religious groups and churches are allowed to discriminate all they want.
That's not entirely true...maybe in Constitutional theory that how it was intended to be, but that's not how it typically plays out in modern day America.
Authorities have stepped in numerous times in cases of cults and religious extremism when they've deemed those organizations to be a safety risk to either the members, or the children of members.
For example, if a cult is fostering an environment which has the potential to cause harm to children, authorities have stepped in...now, whether that's right or wrong in a case where no actual harm has been done
yet is a completely different topic of discussion.
Ultimately, it reflects a larger double standard by our government/society today.
The people who have absolutely no problem taking a shot a Christianity are the same people that say "well, we have to be tolerant" when it pertains to other religions...I don't know if it's a case where people think they're sticking up for the little guy or what...
Look no further than the SSM conversations.
When a Christian church wants to refuse to marry gay couples, the get the label of bigot, etc... Governments use crafty loopholes like the attempted Washington State & New Jersey bills that proposed that if a Church rents out its facilities to straight couples for a fee, then it must also rent its facilities out for a gay wedding as well (using the public accommodation argument).
However, you never seem to hear any scrutiny about mosques refusing to marry gay couples, you never really hear them labeled as bigots (even though the treatment of gays in predominant Muslim countries is far worse than what it is in predominant Christian countries).
It almost seems like when the topic is separation of church and state, if the religion being discussed is Islam, liberals temporarily take the same stance (on what it means) that republicans take when they discuss Christianity.
By that I mean:
Christianity = Separation is all about what they can't make society do
Islam = Separation is all about what society can't make them do.
As an Atheist, I'm not trying to play favorites here...however, I do think the outrage that some Christians have pertaining to the double standards is warranted.