Does the First Amendment protect atheism

Bill Barr's speech at Notre Dame has started me thinking about the following question: Does the First Amendment protect atheism?

The so-called Religious Clauses of the First Amendment read:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;

By definition, atheism is not a religion, but rather the absence of religion. So, is the absence of religion protected by the Religious Clauses of the First Amendment?

In a concurring opinion in McCreary County v. American Civil Liberties Union of Ky., Justice Sandra Day O'Connor wrote:

The Religion Clauses ... protect adherents of all religions, as well as those who believe in no religion at all.

To the modern sensibility, the first of the Religious Clauses, the so-called Establishment Clause ("Congress shall make no law respecting an establishment of religion") seems to suggest that the government cannot prefer religion over irreligion. A strong argument can be made, however, that the intention of the Founders in writing the Establishment Clause was not to prevent Congress from preferring religion over irreligion, but from preferring one religion over another ("establishing" one religion as the state religion). This was done, so the argument would go, in order to prevent what happened in England, where the Church of England (or Anglicanism) was the established church (or official church) of the state. After all, one of the main reasons why colonists left England for America was to avoid persecution for adhering to Christian sects (for example, Puritanism) other than official Anglicanism.

This was the view, for example, of Supreme Court Justice Joseph Story, who wrote in his Commentaries on the Constitution of the United States, first published in 1833:

The real object of the First Amendment was, not to countenance, much less to advance Mahometanism, or Judaism, or infidelity [i.e., atheism], by prostrating Christianity; but to exclude all rivalry among Christian sects, and to prevent any national ecclesiastical establishment, which should give to an hierarchy the exclusive patronage of the national government.

If this second interpretation of the Establishment Clause is deemed correct (and, AFAIK, there is nothing to prevent the SCOTUS from reversing Justice O'Connor's opinion and so deeming), then the First Amendment would provide no protection for atheism, which is not a religion. For more discussion, see here.