Pennsylvania's religious test in its Constitution written in 1776 illustrates why I am suspicious of viewing the Founding (as it regards religion, but other important issues as well) through the lens of federalism. The original Constitution was extremely limited in power and left the states lots of room to engage in practices entirely contrary to Founding ideals -- the worst practice, of course, being slavery.
The Founders separated Church and State at the federal level: The unamended Constitution abolished federal religious tests and left religion entirely unempowered in a Constitution of limited enumerated powers. The amended Constitution prohibited a federal establishment and guaranteed against federal free exercise violations (things that most agreed the federal government didn't even have the enumerated power to do under the unamended Constitution). But they left the states free to violate free exercise, erect establishments and pass religious tests. While a few notable founders (Washington and Adams) thought a mild establishment didn't violate "the rights of conscience" (while Jefferson and Madison thought all establishment did), all notable Founders agreed that free exercise ought to apply universally (to religions, whether Christian or not) and that all such religious tests violated the rights of conscience. States, alas, under the original power scheme, were permitted to violate the rights of conscience. But make no mistake, when states did these things like passing a religious test for holding public office, our Founders viewed this as violating the natural rights enunciated in the Declaration of Independence.
Enter PA's original Constitution which Ben Franklin helped pen. The Constitution contained the following religious test:
And each member, before he takes his seat, shall make and subscribe the following declaration, viz:
I do believe in one God, the creator and governor of the universe, the rewarder of the good and the punisher of the wicked. And I do acknowledge the Scriptures of the Old and New Testament to be given by Divine inspiration.
Yet, Franklin, who helped pen that document, despised such test. As he wrote in a letter to John Calder:
I agreed with you in Sentiments concerning the Old Testament, and thought the Clause in our Constitution, which required the Members of Assembly to declare their belief that the whole of it was given by divine Inspiration, had better have been omitted. That I had opposed the Clause but being overpower'd by Numbers, and fearing might in future times be grafted on [it, I Pre]vailed to have the additional Clause that no [further or more ex]tended Profession of Faith should ever [be exacted. I ob]serv'd to you, too, that the Evil of it was [the less, as no In]habitant, nor any Officer of Government except the Members of Assembly, were oblig'd to make that Declaration. So much for that Letter. To which I may now add, that the[re are] several Things in the old Testament impossible to be given by divine Inspiration, such as the Approbation ascrib'd to the Angel of the Lord, of that abominably wicked and detestable Action of Jael the Wife of Heber the Kenite. If the rest of the Book were like that, I should rather suppose it given by Inspiration from another Quarter, and renounce the whole.
Franklin clearly had good reason to be against the religious test. He admits in this private letter that he doesn't believe the Bible, in its entirely, was given by divine inspiration, thus would be barred from holding office under it. In 1786, he became governor of PA where he helped repeal such test.
Benjamin Rush -- originally an orthodox Christian, but later converted to universalism, believing all will eventually be saved -- likewise despised PA's religious test. Here are excerpts from two of his letters to English Whig Richard Price (who in turn greatly influenced our key Founders).
In the first, Rush calls such a test "a stain from the American Revolution."
[15 Oct. 1785]
I took the liberty of publishing, with your name, your excellent letter on the test law of Pennsylvania. It has already had a great effect on the minds of many people, and I doubt not will contribute more than anything to repeal that law. Dr. Franklin, who has succeeded Mr. Dickinson as our governor, has expressed his surprise at the continuance of such a law since the peace, and we hope will add the weight of his name to yours to remove such a stain from the American Revolution.
And here he notes that such test was eventually repealed:
[22 Apr. 1786]
I am very happy in being able to inform you that the test law was so far repealed a few weeks ago in Pennsylvania as to confer equal privileges upon every citizen of the state. The success of the friends of humanity in this business should encourage them to persevere in their attempts to enlighten and reform the world. Your letter to me upon the subject of that unjust law was the instrument that cut its last sinew.