If the Founding Fathers though there was to be strict separation between church and state then we likely wouldn't have seen the following then and thereafter:
First, two days AFTER the Danbury Separation letter, Jefferson began attending church services in the House of Representatives.
The following is from the U.S. Library of Congress:
Reserved Seats at Capitol Services
Here is a description, by an early Washington "insider," Margaret Bayard Smith (1778-1844), a writer and social critic and wife of Samuel Harrison Smith, publisher of the National Intelligencer, of Jefferson's attendance at church services in the House of Representatives: "Jefferson during his whole administration was a most regular attendant. The seat he chose the first day sabbath, and the adjoining one, which his private secretary occupied, were ever afterwards by the courtesy of the congregation, left for him."
Church Services in The Old House of Representatives
Church services were held in what is now called Statuary Hall from 1807 to 1857. The first services in the Capitol, held when the government moved to Washington in the fall of 1800, were conducted in the "hall" of the House in the north wing of the building. In 1801 the House moved to temporary quarters in the south wing, called the "Oven," which it vacated in 1804, returning to the north wing for three years. Services were conducted in the House until after the Civil War. The Speaker's podium was used as the preacher's pulpit.
A Millennialist Sermon Preached in Congress
This sermon on the millennium was preached by the Baltimore Swedenborgian minister, John Hargrove (1750-1839) in the House of Representatives. One of the earliest millennialist sermons preached before Congress was offered on July 4, 1801, by the Reverend David Austin (1759-1831), who at the time considered himself "struck in prophesy under the style of the Joshua of the American Temple." Having proclaimed to his Congressional audience the imminence of the Second Coming of Christ, Austin took up a collection on the floor of the House to support services at "Lady Washington's Chapel" in a nearby hotel where he was teaching that "the seed of the Millennial estate is found in the backbone of the American Revolution."
First Catholic Sermon in the House
On January 8, 1826, Bishop John England (1786-1842) of Charleston, South Carolina, became the first Catholic clergyman to preach in the House of Representatives. The overflow audience included President John Quincy Adams, whose July 4, 1821, speech England rebutted in his sermon.
Woman Preacher in the House (and call for revival!)
In 1827, Harriet Livermore (1788-1868), the daughter and granddaughter of Congressmen, became the second woman to preach in the House of Representatives. The first woman to preach before the House (and probably the first woman to speak officially in Congress under any circumstances) was the English evangelist, Dorothy Ripley (1767-1832), who conducted a service on January 12, 1806. Jefferson and Vice President Aaron Burr were among those in a "crowded audience." Sizing up the congregation, Ripley concluded that "very few" had been born again and broke into an urgent, camp meeting style exhortation, insisting that "Christ's Body was the Bread of Life and His Blood the drink of the righteous."
Communion Service in the Treasury Building
Manasseh Cutler here describes a four-hour communion service in the Treasury Building, conducted by a Presbyterian minister, the Reverend James Laurie: "Attended worship at the Treasury. Mr. Laurie alone. Sacrament. Full assembly. Three tables; service very solemn; nearly four hours."
Adams's Description of a Church Service in the Supreme Court
John Quincy Adams here describes the Reverend James Laurie, pastor of a Presbyterian Church that had settled into the Treasury Building, preaching to an overflow audience in the Supreme Court Chamber, which in 1806 was located on the ground floor of the Capitol.
The Old Supreme Court Chamber
Description of church services in the Supreme Court chamber by Manasseh Cutler (1804) and John Quincy Adams (1806) indicate that services were held in the Court soon after the government moved to Washington in 1800.
Church Services in Congress after the Civil War
Charles Boynton (1806-1883) was in 1867 chaplain of the House of Representatives and organizing pastor of the First Congregational Church in Washington, which was trying at that time to build its own sanctuary. In the meantime the church, as Boynton informed potential donors, was holding services "at the Hall of Representatives" where "the audience is the largest in town. . . .nearly 2000 assembled every Sabbath" for services, making the congregation in the House the "largest Protestant Sabbath audience then in the United States." The First Congregational Church met in the House from 1865 to 1868.
House of Representatives, After the Civil War
The House moved to its current location on the south side of the Capitol in 1857. It contained the "largest Protestant Sabbath audience" in the United States when the First Congregational Church of Washington held services there from 1865 to 1868.
Compliments: Library of Congress
http://www.loc.gov/exhibits/religion/rel06-2.html
I think it's safe to say we can know the measure of the Founding Father's beliefs by their actions above. Their actions do not jive well with a strict "separation of church and state" doctrine like we know it today.