The Establishment Clause is something of an outlier in constitutional jurisprudence.
First, the Establishment Clause, as ratified in 1791, was a federalism provision. It prevented Congress from interfering with state establishments of religion. That provision suggests that states can have established religions, and that Congress cannot disestablish any of those religions. As all know, there were several established churches at the time of the founding. And if tradition means anything, then practices from 1791 are directly relevant to this question.
Second, as Justice Thomas has observed, such a federalism provision resists incorporation. I've not seen any compelling evidence from debates during the 39th Congress suggesting that the Fourteenth Amendment would place the states under the strictures of the Establishment Clause. (And if the Section 3 debates has taught us anything, the only relevant speeches that matter to understand the Fourteenth Amendments are remarks from congressional republicans in a narrow two-year window.) To be sure, there were comments about the freedom of conscience, perhaps as a privilege or immunity of citizenship, but not about the Establishment Clause in particular–and certainly not about how the Warren Court understood the Establishment Clause. And by the 1860s, all of the Established Churches had been disestablished. But as a practical matter, it was never clear to me how the Establishment Clause could even be incorporated as a privilege or immunity of citizenship, or even as a liberty protected by the Due Process Clause.
Third, the Establishment Clause doctrine developed in the Twentieth Century was based on a misreading of Jefferson's letter to the Danbury Baptist, and ignored the overwhelming amount of evidence that others in the founding generation did not share Jefferson's views. (See Justice Scalia's dissents in Lee v. Weisman and McCreary County.) And there was no attempt to graft it in how religion was understood in the 1860s.
Fourth, the Establishment Clause has had anomalous effects in other areas of the law, such as "taxpayer" standing and "offended observer" standing. (I've referred to these adjustments as "epicycles.") These doctrines were invented to ensure there was standing to consider cases based on invented doctrines. Legal fictions all the way down. Really, all we are left with is a stare decisis defense of Establishment Clause cases. We know how much that is worth.
The Court has begun to correct course. The Court (effectively) overruled the Lemon test in Kennedy, favoring a "text, history, and tradition" approach. No more concerns about "purpose" or "entanglement." American Legion cabined McCreary County with regard to public displays of religion. I don't think any such new cases are even in the pipeline. Town of Greece cabined Lee v. Weisman for public prayer cases. I've seen some arguments that prayer in school may be in play, if done in a voluntary, separate setting. And Carson v. Makin has largely addressed funding of religious institutions. Providing the funding indirectly, instead of directly, gets around most issues. Blaine Amendments are on precarious ground, even if not formally declared unconstitutional.
What remains of the Establishment Clause going forward? I think cases of actual coercion are still viable. In my view, those sorts of claims always seemed more grounded in Free Exercise doctrine than in Establishment Clause doctrine. That is, coercing a person to engage in any particular faith is itself a violation of that person's own rights of conscience. Justice Gorsuch's opinion in Kennedy recognized this principle. That sort of argument works even for an atheist, whose system of conscience is to have no religion at all.
There are also cases where the government prefers one particular religion, or disfavors a particular religion. We saw these claims raised during the travel ban litigation–that is, the policy expressed a disfavor (animus) towards Islam. At the time, I thought these claims sounded in the Free Exercise Clause, like in Lukumi. That is, the government was burdening the rights of Muslims because of their religion. But of course, that argument would not work with the travel ban, because non-citizens seeking entry to the United States could not assert a free-standing Free Exercise claim. Instead, they had to assert some sort of structural Establishment Clause against the federal government. That argument never made much sense to me.
In candor, there is not much Establishment Clause caselaw left over after Kennedy, Carson, Town of Greece, and American Legion. A union of church and state that would have been unconstitutional a generation ago is now constitutionally mandated–Justice Sotomayor's Carson dissent makes this point directly. And what little doctrine exists is probably better conceptualized as Free Exercise jurisprudence.
So I pose the question: can the Establishment Clause be unincorporated? The federal government would remain subject to the clause–perhaps even subject to modern doctrine. National policy would still have to be religiously neutral. But states would only be subject to the strictures of the Free Exercise Clause. The originalist case for incorporating the Establishment Clause never made sense. That caselaw has engendered massive and unending controversies. And it has distorted other areas of caselaw. Whatever concrete reliance interests could be addressed through a properly-understood Free Exercise Clause. The only claims that would fall out would be those that have no basis on text, history, or tradition.
Readers of this post may be rolling there eyes, but this is how change start. Seeds are planted and things grow. There is some scholarship defending the incorporation of the Establishment Clause by Kurt Lash and Fred Gedicks. Those might be good places to start thinking about the issue.
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