Timothy Sandefur has been giving the Panda's Thumb posters an excellent lesson in constitutional law. The topic is whether the Establishment Clause is properly incorporated via the 14th Amendment as applying against state governments. And Sandefur heavily relies on the work on Akhil Amar's excellent book (which I just got yesterday) on the Bill of Rights.
I think both Sandefur and Amar make a little bit too much of the notion that the Establishment Clause was intended to be a federalism only provision, and that one important part of that clause was to guarantee the rights of states to make their own establishments. States were free to enact establishments as an incidental effect of the entire First Amendment applying only to Congress, just as states were free to violate free exercise and free speech norms as an incidental effect of the First Amendment's restraint on the Federal government only.
To inject some natural law into this analysis, both clauses of the First Amendment and Article VI's no religious test clause were written, however imperfectly, to secure the unalienable free and equal rights of conscience against federal government violations. States, on their own, were morally obligated (but not legally obligated under federal law) to secure such natural rights. And Jefferson thought they'd do a better job of this than would the federal government.
By the time the 14th Amendment was passed the federal government would have the jurisdiction over state violations of natural rights under the Privileges or Immunities, Due Process and Equal Protection clauses of the 14th.
Okay, the bottom line: Is the Establishment Clause properly incorporated, and if so, in what way? As Amar shows in his excellent book, the answer to this question is in large part semantical. For instance, Amar demonstrates the doctrine of incorporation to be proper. But currently the Court has incorporation taking place under the "Due Process" Clause when in reality it properly should be done under the "Privileges or Immunities" Clause. Whether the Establishment Clause is properly incorporated at all, much of what the Supreme Court has it doing -- including forbidding states from officially establishing any church -- would be proper under the Free Exercise and Equal Protection clauses.
In order for the Establishment Clause to be properly incorporated, it must relate to protecting some kind of individual right. The Free Exercise Clause obviously relates to protecting an individual right. Both Sandefur and Justice Thomas generously discuss how the Free Exercise Clause alone could handle most of these claims: Quoting Justice Thomas, “the Establishment Clause, [if incorporated]…would probably cover little more than the Free Exercise Clause.”
The problem with Sandefur's and Thomas's analysis is that, while it address liberty, it ignores equality of conscience. When our founders used the term "liberty" it very often appeared in conjunction with the term "equality." And Jefferson and Madison's writings make it clear that men, by nature, have not only free, but also equal rights of conscience. From Madison's Memorial and Remonstrance, quoting the VA Declaration of Rights [my emphasis on the word "equal" and its variations]:
Because the Bill violates that equality which ought to be the basis of every law, and which is more indispensible, in proportion as the validity or expediency of any law is more liable to be impeached. If "all men are by nature equally free and independent," [Virginia Declaration of Rights, art. 1] all men are to be considered as entering into Society on equal conditions; as relinquishing no more, and therefore retaining no less, one than another, of their natural rights. Above all are they to be considered as retaining an "equal title to the free exercise of Religion according to the dictates of Conscience." [Virginia Declaration of Rights, art. 16] Whilst we assert for ourselves a freedom to embrace, to profess and to observe the Religion which we believe to be of divine origin, we cannot deny an equal freedom to those whose minds have not yet yielded to the evidence which has convinced us.
And from Madison's original draft of the First Amendment:
The Civil Rights of none shall be abridged on account of religious belief or worship, nor shall any national religion be established, nor shall the full and equal rights of conscience be in any manner, nor on any pretext infringed. No state shall violate the equal rights of conscience or the freedom of the press, or the trial by jury in criminal cases.
Akhil Amar does discuss the equality aspect of religion under the 14th Amendment. Because the Free Exercise Clause appears to be a "liberty," not an "equality" clause, perhaps the Establishment Clause, not the Free Exercise Clause is the more proper place for securing this equality norm. When I saw Philip Hamburger speak at Princeton University, he noted, "the Establishment Clause is not an equal protection clause" to which a subsequent speaker retorted -- one of the cleverest retorts I've heard in my life, "yes, but the Equal Protection Clause is an equal protection clause." I think Amar would agree:
Perhaps the greatest elaboration came from Thomas Cooley's influential 1868 treatise. Under prevailing state constitutions, wrote Cooley, states generally could not enact "[a]ny law respecting an establishment of religion....There is not religious liberty where any one sect is favored by the State....It is not toleration which is established in our system, but religious equality." Even a noncoercive establishment, Cooley suggested, violated principles of religious liberty and religious equality -- violated norms of equal rights and privileges. And once we see this, it turns out that the question -- should we incorporate the establishment clause? -- may not matter all that much, because even if we did not, principles of religious liberty and equality could be vindicated via the free-exercise clause (whose text, history, and logic make it a paradigmatic case for incorporation) and the equal protection clause (which frowns on state laws that unjustifiably single out some folks for special privileges and relegate others to second-class status). Surely Alabama could not adopt a state motto proclaiming itself "the White Supremacy State"; such a motto would offend basic principles of equal citizenship and equal protection. And so a law that proclaimed Utah a Mormon state should be suspect whether we call this a violation of establishment principles, free-exercise principles, equal-protection principles, equal-citizenship principles, or religious-liberty principles. Once we remember that we are not incorporating clauses mechanically but reconstructing rights, we reach the unsurprising conclusion that our basic touchstones should be the animating Fourteenth Amendment ideals of liberty and equality. pp. 253-4
In other words, a great deal of separation of Church & State, perhaps not what the ACLU desires, but nonetheless drawing a sharp distinction between Church & State, is required to respect the full free and equal rights of conscience, regardless of which particular combination of clauses is the proper source of the norms. As with incorporation, the fact that the norms themselves are legitimately applied, not necessarily where the Court has the norms coming from is what's most important.
And even the concept of "equal protection" -- which we regard as a substantive norm of equality -- may not be coming from the proper clause. The text of the equal protection clause, like the due process clause, seems to be entirely procedural, not substantive. The law must equally apply whatever general laws are on the books. But it is also unquestionable that the 14th Amendment contains substantive norms of liberty and equality as well. The substantive norms probably are properly contained within the "privileges or immunities" clause, the procedural norms, the due process and equal protection clauses. After the Slaughterhouse Cases unfairly eviscerated the privileges or immunities clause, when it came time to channeling substantive norms of liberty and equality, the court looked to where the words "liberty" and "equality" appeared in the text of the constitution: the due process and equal protection clauses -- maybe not the most proper places, but absent the privilege or immunities clause, the next most logical places.