States have power to regulate commerce, as does the federal government when that commerce has an impact on interstate commerce. Federal government power to enforce equal protection under the 5thand Fourteenth Amendments cannot trump individual or private business rights. The federal government can only enforce equal protection against state and federal governments. States can enforce their own equal protection laws against individuals and private businesses, but those laws must meet U.S. Constitutional standards.
The federal and most, if not all state RFRA’s require that government laws and acts that substantially infringe on religious practices must be justified by government by showing that it is narrowly tailored to meet a compelling government interest (strict scrutiny). The federal and state governments can statutorily bind themselves to a rule which, in effect, provides greater protection than the First Amendment. The federal RFRA applies only to the federal government. A state law applies only in that state. In the absence of a state RFRA, the state and federal governments must meet only the lenient test of the Smith case. If there is a state RFRA the issue would then be whether the anti-discrimination statute can meet the state statutorily mandated strict scrutiny test. This test gives the business owner more, but not absolute protection. Arguably, preventing discrimination on the basis of sexual orientation by businesses is a compelling governmental interest. If the statute is carefully written to be neutral and general, serves a compelling interest and is narrowly tailored (to minimize damaged to religious rights) it could overcome the RFRA. Again, the business loses.