Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof
Amendment I
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the Government for a redress of grievances.
http://www.archives.gov/exhibits/charters/bill_of_rights_transcript.html
These two clauses are interrelated and off set each other to a degree. The establishment clause says they will be no FEDERAL Religion (Till the 14th amendment was adopted after the Civil War, the Federal Bill of Rights only applied to the Federal Government not the States) AND the Free Exercise clause forbade the Federal Government from imposing any restrictions on any religion.
Now the Supreme Court has had problems with these two clauses, but only since the 14th amendment was passed (and mostly since the decision to incorporate the First Amendment into the 14th starting in the 1920s). If a State passes a law that bans something, that a religion also ban, is that a violation of the Establishment clause? The Court has generally said no, for that would mean Murder, which is banned by most religions, could not be made a crime for that would be establishment of religion.
Thus the Court has taken a policy to look at the law being challenged and if any reason could show it is NOT religious in nature, it would be upheld as NOT being a violation of the Establishment clause (Thus the various restrictions on abortion have been held to be constitutional even if based in Religion beliefs).
Please note the Right to Abortion is independent of the First, it has been upheld as a right under Constitution that existed at the time of passage of the Bill of Rights. The Bill of Rights is NOT an exclusive list and thus Rights exist that are NOT listed in the Bill of Rights. The Right to Abortion existed at the time the Bill of Rights was adopted and as such is one of those rights preserved even through it was not listed under the Bill of Rights. Please note like most of the Rights under the Bill of Rights the right to an abortion is a right subject to reasonable restrictions (in fact Roe vs Wade restrictions on when a state can impose restrictions, followed the English Common Law Restrictions that existed at the time of the Bill of Rights. Those Restrictions were ancient, but appears to follow the restrictions mentioned by St Augustine in the 400s. St Augustine drew his restrictions from the practice of ancient Israel, Greece and Rome. St Augustine restrictions were the Catholic Rule on Abortions, till pressure from the Medical Community, who wanted to take aver births and abortions from mid-wives where it had been for over 2000 years, lead to the change to the modern Catholic Doctrine in 1869).
The Free Exercise Clause has also come under attack by the Supreme Court, the Peyote case is the classic case. In the Peyote certain Native America Tribes said the federal ban on Peyote interfered with their religion. The Supreme Court actually accepted that argument but then rule that if a ban in general in nature, not aimed at a particular religion, it is still effective even on practitioners of that religion. Thus the Federal Ban on Peyote was constitutional even if it interfered with the religion of Native Americans.
On top of this is the Religious discrimination ban added to the 1964 Civil Rights act in the 1990s. Since the 1990s one's religion is a protected class of people (Which include atheism as a religion, the Supreme Court has long ruled Religion is more then a belief or non belief in God, it is a world view, thus under the first Atheism is a religion). As a protected class, it can be argued that a law protecting Gays from discrimination is off set by the Civil Rights Act protection of one's religious beliefs. Furthermore, as a general rule, most State Civil Rights Acts provides exemptions based on religion (The Federal Civil Rights Acts do NOT make being gay a protected class so it is not a factor in this case).
Thus, this couple first has to get around any restrictions imposed by the California Civil Rights Acts as to religion, then get around the Free Exercise Clause of the US Constitution. Not impossible, but I doubt he will prevail.
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