In his dissent to Obergefell, Justice Clarence Thomas raised the specter of a conflict between First Amendment rights and the Supreme Court's concept of liberty under the Fourteenth Amendment.
Aside from undermining the political processes that protect our liberty, the majority’s decision threatens the religious liberty our Nation has long sought to protect...
Numerous amici—even some not supporting the States—have cautioned the Court that its decision here will “have unavoidable and wide-ranging implications for religious liberty.” Brief for General Conference of Seventh-Day Adventists et al. as Amici Curiae 5. In our society, marriage is not simply a governmental institution; it is a religious institution as well. Id., at 7. Today’s decision might change the former, but it cannot change the latter. It appears all but inevitable that the two will come into conflict, particularly as individuals and churches are confronted with demands to participate in and endorse civil marriages between same-sex couples.
Justice Thomas does not specify from where exactly these "demands to participate in and endorse civil marriages" will come, however. If those demands are purely social, from individuals and other religious groups, then they are of no concern to the Supreme Court. The First Amendment protects individual free exercise from government action, not from public criticism or social pressure. Unless the government starts demanding that churches perform certain kinds of weddings (it doesn't currently, has never in the past, and won't in the future), no First Amendment infringement seems possible.
But still, this weak argument aside, could the Supreme Court have created the possibility of a conflict between the First and Fourteenth Amendments? In previous writing I have assumed that such a conflict might be possible (but nevertheless the Fourteenth should triumph over the First). But I have thought more about it and now I'm not so sure a conflict is really possible.
Both the First and Fourteenth Amendments constrain government action. The First Amendment says the government can't infringe our rights to speech, petition, assembly, and religion. And not only is our religious free exercise protected, but we are also protected from any formal establishment of a state religion which might exclude non-believers. The Fourteenth Amendment, for its part, requires that the government provide due process before any deprivation of life, liberty, or property, and that it provide equal protection under the law.
So how, exactly, can these two amendments conflict? The right of someone else to get a state license for their marriage doesn't interfere at all with anyone's personal beliefs. It doesn't compel an individual, private citizen to act in any sort of way, either. Churches can still turn gay couples away. Ministers can refuse to solemnize certain marriages they don't condone. Parishioners can shun whoever they find distasteful. Obergefell changed none of that.
Opponents of Obergefell conceive of only two possible scenarios where a conflict between the First and the Fourteenth Amendment can arise.
The first is the possibility that discriminatory religious organizations might lose tax exempt status. In the case of Bob Jones University v. United States, 461 U.S. 574 (1983), a religious school lost tax exempt status because it prohibited interracial dating among students. This was such a flagrant violation of the legitimate government policy of integration and anti-discrimination that the IRS revoked the school's tax privileges. There's an important distinction here: tax exempt status is not a religious right. It is a privilege extended by the government consistent with larger public policies. Whether a religious organization is tax exempt or not has no effect on the individual religious beliefs of its members or its administration. They are free, as individuals, to oppose interracial (or same-sex) marriages in their individual lives, but they can't discriminate in public and expect to receive public benefits for it.
The other situation is the now-familiar case of county clerks in Kentucky. They are denying marriage licenses either to all couples or just to same-sex couples in protest of Obergefell. The clerks argue that their First Amendment religious rights are infringed by having to issue licenses to couples they dislike. But courts have never recognized a right of public officials to exercise their religious beliefs when acting in their official, public capacity. Clerks can certainly believe whatever they want, and in their private lives away from work they can shun anyone they believe is sinful. But when they're at work as county clerks, they are the government. If there is any constitutional conflict at play, it's perhaps an internal conflict within the First Amendment between the Establishment Clause and the Free Exercise Clause. The Establishment Clause prevents the imposition of religious whim by government officials in order to preserve equality for all. In that way, the First Amendment and the Fourteenth Amendment work in conjunction. They don't conflict.
The Supreme Court has previously explained how the First Amendment and Fourteenth Amendment actually work together to preserve individual liberty from government oppression. In West Virginia State Board of Education v. Barnette, the Court struck down mandatory recitations of the Pledge of Allegiance in public schools. The Barnettes, a family of Jehovah's Witnesses, argued that their personal beliefs relegated the authority of the state below the authority of god. Therefore they could not swear an oath or allegiance to the national flag, as mandated by the public school system. They argued that under both the First Amendment and the Fourteenth Amendment, the government could not single out their children for punishment when they refused to say the Pledge due to their religious convictions.
The Supreme Court agreed with the Barnettes. In doing so, the Justices noted that the First Amendment and the Fourteenth Amendment actually work together, protecting the liberties of individuals from government intrusion and compulsion. The Fourteenth Amendment, rather than an enemy of religious exercise and free speech rights, is a tool for their protection:
In weighing arguments of the parties it is important to distinguish between the due process clause of the Fourteenth Amendment as an instrument for transmitting the principles of the First Amendment and those cases in which it is applied for its own sake. The test of legislation which collides with the Fourteenth Amendment, because it also collides with the principles of the First, is much more definite than the test when only the Fourteenth is involved. Much of the vagueness of the due process clause disappears when the specific prohibitions of the First become its standard. The right of a State to regulate, for example, a public utility may well include, so far as the due process test is concerned, power to impose all of the restrictions which a legislature may have a "rational basis" for adopting. But freedoms of speech and of press, of assembly, and of worship may not be infringed on such slender grounds. They are susceptible of restriction only to prevent grave and immediate danger to interests which the State may lawfully protect. It is important to note that while it is the Fourteenth Amendment which bears directly upon the State it is the more specific limiting principles of the First Amendment that finally govern this case.
319 U.S. 624, 639 (1943).
In the two situations above, where modern proponents of theocracy foresee a conflict between the First and Fourteenth Amendments, there is no government action infringing on free exercise. The revocation of tax exempt status does not compel a change in religious beliefs. It may incentivize religious schools to stop discriminating, but it does not force them to do so. They can continue to discriminate, but they will have to pay taxes in the meantime, just like religious individuals who are also free to discriminate but don't get a tax break for doing so.
And the provision of marriage licenses to same-sex couples doesn't stop religious individuals or organizations from hating and shunning gay people or politically opposing such unions. But county clerks do not act as individuals. They are the government, and as such, they cannot use religious free exercise as an excuse to treat some citizens differently and deny government services to them. When they do so, they create a conflict not between the Free Exercise Clause and the Fourteenth Amendment, but between the government and the Establishment Clause.