Associate Justice Story was a child when the Constitution was being written and was merely ten years old when it was adopted (1789). Undoubtedly, his understanding of the intentions of our nation's founders was from second-hand sources and hearsay evidence that would not bear scrutiny in a court of law.
Furthermore, Story was from Massachusetts, the state that was the very last state to disestablish the church and bring its state constitution into line with the federal constitution. Massachusetts did not disestablish its church until 1833 -- the same year that Story's commentary was published. On the topic of church-state separation, both Story and his native state were obviously out-of-step with the rest of the people in the country.
I've been suggesting to Jeffress that he read source documents instead of second-hand documents for his understanding of the intentions of the founding fathers and the mindset of revolutionary America. The primary source to read is James Madison's Memorial and Remonstrance. Madison is the primary author of the Constitution and of the Bill of Rights.
Jeffress would know that if he knew his Baptist history. It was Baptist evangelist John Leland and the Baptists in Virginia who convinced Madison that he had better add the First Amendment if he wanted to get the Constitution ratified in Virginia. After the U.S. Constitution was adopted, Leland wrote a pamphlet entitled "The Rights of Conscience Inalienable" (1791) that explained the intention of the First Amendment and Article VI of the Constitution:
"The federal constitution certainly had the advantage of any of the state constitutions, in being made by the wisest men in the whole nation, and after an experiment of a number of year's trial upon republican principles; and that constitution forbids Congress ever to establish any kind of religion, or to require any kind of religious test to qualify for any office in any department of federal government. Let a man be Pagan, Turk, Jew or Christian, he is eligible to any post in that government."(L. F. Greene, ed. The Writings of John Leland. New York: Arno Press, 1969, p. 191)
Regarding the inequities of the state constitution in Massachusetts, here's what Leland said to the Massachusetts House of Representatives in 1811:
Government should be so fixed, that Pagans, Turks, Jews and Christians, should be equally protected in their rights. The government of Massachusetts, is, however, differently formed; under the existing constitution, it is not possible for the general court, to place religion upon its proper footing. (p. 358)In times past I could only quote the references and hope that readers would be able to find a copy of Leland's writings in a local library. Today, anyone can download the book from Google Books and check the reference for themselves at their leisure both online and on their own laptops and computers. So there is no longer any excuse for Baptists to not be familiar with the writings of the Baptist leaders who led the struggle for religious liberty in America.
Here's a link to "The Writings of the Late Elder John Leland." (1844)
Here's a link to Massachusetts Baptist leader Isaac Backus' "Appeal to the Public for Religious Liberty: Against the Oppressions of the Present Day" (1773).