To get right to the point: Mr. Hacker does not disagree that the Establishment Clause would, in the absence of the Fourteenth Amendment, have prohibited Congress from passing a nationwide religion law like RFRA. He believes, however, that the Fourteenth Amendment has in part repealed the First.
Of course, he doesn't want to say repealed. The language of repeal is not pleasant to the ears of those who would like to forget about First Amendment antidisestablishmentarianism. The Fourteenth Amendment did not "repeal any aspect of the text of the [Establishment] Clause," Hacker says, but only "change[d] profoundly the meaning of [its] words.(1) If, however, statute A means x and y, and statute B (enacted later) provides "x shall no longer be the law of the land," it makes no difference whether we say that B partially repealed A or merely "changed profoundly the meaning of [its] words."(2) If, moreover, B does not expressly provide that x shall no longer be the law of the land -- if, rather, there is merely a debated question of whether B should be so interpreted -- then the question, for good or ill, is whether to read B as having partially repealed A.
Dodging the word repeal, in other words, does not alter the question. No one had ever supposed that the Fourteenth Amendment rescinded any of the foundational prohibitions laid upon Congress in the First through Eighth Amendments. Until now -- for this is just what Mr. Hacker says the Fourteenth Amendment did. Of course, it is possible to read the Fourteenth Amendment this way, but Mr. Hacker's arguments in defense of this position would have been far stronger if he had better appreciated the principles of religious liberty underlying -- both in 1789 and in the present day -- the Establishment Clause.
The basic premise of Mr. Hacker's argument is an injustice he does to the First Amendment. As to the twofold core meaning of the Establishment Clause, there is no serious disagreement. The Clause prevented Congress both from establishing a national religion and from interfering with certain local religion laws, defended by their champions in the name of religious freedom but condemned by their detractors as establishments.(3) The paradigm case here was the ecclesiastical system common throughout New England, where each town was permitted to install by majority vote a Protestant ministry to be supported by tax revenues (with exemptions provided for some dissidents).(4) This second aspect of the Establishment Clause, prohibiting Congress from interfering with local pro-religion laws, is its antidisestablishmentarian component.
Mr. Hacker evidently derived from the historical sections of my article a very disparaging view of First Amendment antidisestablishmentarianism. He...