“As an initial matter, the Clause probably prohibits Congress from establishing a national religion.” –Justice Clarence Thomas, in his concurring opinion in Greece v. Galloway
“Probably”? As if the May 5, 2014 Town of Greece v. Galloway decision, upholding prayers said at the beginning of legislative meetings, didn’t upset strict separationists enough, Justice Clarence Thomas’s radically originalist concurring opinion was enough to bring on shouts for an exorcism. To the contrary, Thomas’s reasoning about the First Amendment establishment clause is the most rational way to preserve liberty, by recognizing the institutional principle of federalism as well as the individual right of religious free exercise. This becomes clear once we see this opinion in light of his earlier, lengthier establishment opinions.
But even this brief opinion, as with many of Thomas’s other concurrences and dissents, is an education in the Constitution. In Greece a coalition of justices upholds the town’s prayer practice as in line with Establishment Clause precedent for different vaguely nonpreferentialist reasons. Justice Alito’s concurrence responds to the dissenters. Justice Scalia concurs with him and also concurs in part with Thomas. Four dissenters (with Justice Breyer filing his own separate dissent) maintain that the prayers were too sectarian, arbitrary, and coercive to be reconciled with precedent. They reflect the “separationist” argument typified in the crèche and menorah display case of County of Allegheny v. ACLU, Greater Pittsburgh Chapter (1989).
Impatient with splitting hairs, Thomas would decapitate the line of earlier cases in an intellectually liberating move that should delight even his ideological opponents. Thomas first brushes aside the accepted incorporation doctrines concerning the 14th Amendment, which argue variously for total or partial incorporation of the Bill of Rights, including notions of “due process” or “fundamental fairness.”
Basing his analysis on recent scholarship, Thomas maintains that neither the founders nor the drafters of the 14th Amendment had in mind the incorporation of the Establishment Clause of the First Amendment. At least six States at the time of the founding had established churches, with Massachusetts keeping its until 1833. The Establishment Clause, Thomas concludes, was actually intended to protect these State-established churches against a uniform law of Congress; it thereby expressed the fundamental structural constitutional principle of federalism (and the Tenth Amendment), thus leaving religious issues to the States. (By contrast, the free exercise clause, he argues, does apply to the States .)
This recognition of the scholarly dispute is one reason for the “probably” in Thomas’s concurring opinion. In fact, he had already made the same observation in the Newdow Pledge of Allegiance case (Elk Grove Unified School District v. Newdow, 2004): “As a textual matter, this Clause probably prohibits Congress from establishing a national religion. But see P. Hamburger, Separation of Church and State 106, n. 40 (2002) (citing sources).” Comparing the two “probably” sentences gets us to the core of his Establishment Clause argument. In Newdow, he had focused on the significant contribution of Philip Hamburger in his Separation of Church and State (2000)—available online here or condensed in article form here. When we check the Hamburger footnote that Thomas refers to (“But see P. Hamburger….) we see a dispute over the meaning of the scope of the Establishment Clause among thoughtful scholars (106, n. 40). Hamburger himself concludes “Yet the establishment clause also clearly stood in the way of a federal establishment.”  In Newdow Thomas declares “I would take this opportunity to begin the process of rethinking the Establishment Clause.” Greece continues this rethinking.
Moreover, even if one rejects the federalism argument, Thomas adds a challenge for those who would inflate the meaning of the Establishment Clause by emphasizing the “respecting” in “Congress shall make no law respecting an establishment of religion.” In their view, the “respecting” means anything that might remotely have to do with establishment and thereby bolsters the entire separationist school of thought.
Not citing Hamburger here, Thomas’s review of the scholarship in Greece focuses more on Donald Drakeman, Church, State, and Original Intent (2010), in addition to the work by Michael McConnell, Robert Natelson, Leonard Levy, Akhil Amar, Philip Munoz, among others he had drawn on before. “The import of this history is that the relationship between church and state in the fledgling Republic was far from settled at the time of ratification.” Munoz, author of an important study of the differences among the founders on religion, provides a succinct assessment of Drakeman’s strengths and failing:
By adding the word “respecting” to the phrase “Congress shall make no law,” the conference committee appears to have reverse engineered words already present in the Constitution [Article IV, section 6, "The Congress shall have Power to dispose of and make all needful Rules and Regulations respecting the Territory or other Property belonging to the United States."] to make clear that the national government lacked, and that the states retained, all jurisdiction over religious establishments. It was a remarkable piece of constitutional craftsmanship that precluded the national government both from making an establishment and from interfering with the states’ church-state arrangements. Drakeman misses the latter purpose.
Thus, Thomas’s “probably” reflects this scholarly dispute but even more his respect for Hamilton’s argument that the original Constitution was a “bill of rights” (Federalist 84) before it had a Bill of Rights of ten amendments. After all, there is no congressional power enumerated or implied that would allow Congress to establish a state religion in the first place—unless one reads the commerce clause as allowing regulation of trafficking in “strange gods.”
But all this fear of creeping establishment obscures the original understanding’s support for religion’s place—specifically that of the Christian religion—in civic life. Under the aegis of the principles of the Declaration of Independence (“exercise of their inherent natural rights”), religions could flourish, as Washington expressed so beautifully in his letter to the Hebrew Congregation of Newport.
While going to this right source, Justice Kagan misappropriates Washington’s letter in her Greece dissent, by ignoring the “natural rights” reference and turning Washington’s eloquence into what she had earlier called a “norm of religious equality,” a standard that would have dumbfounded Washington. Kagan misses the significance of Washington saying that America stands not merely for religious toleration; “All possess alike liberty of conscience and immunities of citizenship.”
Part of the glory of the American public square is that citizens can see what inspires different members of the community, including their religions. Restrictions on religious expression are not merely violations of rights but also a diminution of common citizenship. Legal blogger Josh Blackman’s personal reflections on public prayer and his growing appreciation of what the prayers of those of a different faith meant to them exemplify how the public square should elevate. This fulfills the purpose of the official, quasi-religious holiday of Thanksgiving. Both remind us that there are not only religious rights but citizen duties as well. The citizen in us should be strong enough to allow those of other faiths (and I like Blackman, grew up in a non-Christian family) to be robust in theirs.
The evening before oral argument in his Supreme Court case, I asked Michael Newdow following a public talk at the University of Maryland whether his theory would require the removal of the Maryland flag behind him. or the elimination of its two crosses in order to avoid giving him offense. Startled, looking back at the flag, he became angry and tried to change the subject by attacking my motives for raising this question. He embodied the intolerance that he claimed to be fighting. In truth, the separationist argument betrays its origins in anti-religious, specifically anti-Catholic motives, as this New Republic editorial (September 2, 1916) boldly proclaims and as Hamburger and Drakeman show in their work on Hugo Black. 
Not for the first time, Justice Thomas appears to be an extremist but is in fact a moderate, a constitutionalist. In the matter of Establishment Clause cases, the extreme that bases itself on the founding protects liberty. By this simple logic it stands to win over his colleagues and help restore religious liberty.
 See, e.g., Alexandra Petri’s May 6 column, “Clarence Thomas’s curious ‘probably.’” http://www.washingtonpost.com/blogs/compost/wp/2014/05/06/clarence-thomass-curious-probably-what-would-the-founders-say/
 See Thomas G. West’s review of Hamburger, “God and Man in America,” Claremont Review of Books (Spring, 2003). http://www.claremontinstitute.org/index.php?act=crbArticle&id=1212#.U3uMKvldWSo
 See the Munoz review of Drakeman, “Block That Metaphor,” Claremont Review of Books, Fall 2010, 49-51. http://www.claremont.org/img/crb/pdf/138907066904_Fall2010CRB.pdf
 Consider only the difference in tone between this letter and Washington’s letter to Catholics, especially in the last sentence. http://teachingamericanhistory.org/library/document/letter-to-the-roman-catholics/
 The horrific scene of the forced conversion of Shylock in Shakespeare’s Merchant of Venice (IV. 1) reflects more the spirit of today’s secularists and separationists. In his dissent in Marsh v. Chambers (1983) following up on his Abington School District v. Schempp concurrence, Justice Brennan declares that “a proper respect for the Framers themselves forbids us to give so static and lifeless a meaning to their work. To my mind, the Court’s focus here on a narrow piece of history is, in a fundamental sense, a betrayal of the purposes of history.” http://www.law.cornell.edu/supremecourt/text/463/783#writing-USSC_CR_0463_0783_ZD Reflecting the historicist Zeitgeist of political orthodoxy, Brennan worships the God of History: Shut up, History explains.