Should Discrimination Ever Be Permitted In the Name of Religious Freedom?

The saga of Indiana’s Religious Freedom Restoration Act has intensified the conversation about religious reasons for discrimination. Are there ever any defensible religiously based reasons for discriminating against a protected class?

One source I consulted on this was the Equal Employment Opportunity Commission guidance on religious discrimination. The following section seems relevant to the matter of competing discrimination claims (religious v. something else):

Thus, a religious organization is not permitted to engage in racially discriminatory hiring by asserting that a tenet of its religious beliefs is not associating with people of other races.  Similarly, a religious organization is not permitted to deny fringe benefits to married women but not to married men by asserting a religiously based view that only men can be the head of a household.

Sex Discrimination Not Excused

Justina works at Tots Day Care Center.  Tots is run by a religious organization that believes that, while women may work outside of the home if they are single or have their husband’s permission, men should be the heads of their households and the primary providers for their families.  Believing that men shoulder a greater financial responsibility than women, the organization pays female teachers less than male teachers.  The organization’s practice of unequal pay based on sex constitutes unlawful discrimination.[49]

The footnote for the case of Justina goes to the following court decision:

EEOC v. Fremont Christian Sch., 781 F.2d 1362 (9th Cir. 1986) (religious school violated Title VII and the Equal Pay Act when it provided “head of household” health insurance benefits only to single persons and married men).

Think about it. There may be bakers and florists and photographers who still believe miscegenation is wrong for religious reasons. Should a photographer’s religious objection to taking pictures at a wedding of two people of different races be protected? Should the act of refusing to take pictures be protected behavior? The EEOC suggest that the answer would be no.
To the example above. If owners of a daycare are forced to pay equal wages to men and women in violation of their religious beliefs, do the owners suffer religious discrimination? According to EEOC v. Fremont Christian, the Christian school engaged in unlawful discrimination by failing to treat married women the same as married men. Thus, sex discrimination trumps religious freedom.
The open question is does the government’s interest in non-discrimination override religious reasons for such discrimination. If so, what set of facts could lead a court to say certain religious objections trump the government’s interest in equal treatment?