Well....I was thinking more along the idea of how Jefferson thought that such things as the virgin birth, Jesus' miracles, the Resurrection, etc were horse hockey.
Setting up a separate theology department follows the old Renaissance teaching that theology is the queen of the sciences. Try again.
Jefferson certainly didn't think it the "queen of sciences". He didn't allow for a publicly-funded divinity school on the Univ of Virginia because he thought it was a violation of the First Amendment. He was keen, however, on giving the divinity students access to the U of Va campus (and students) because he thought it might "liberalize and neutralize their prejudices, and make the general religion a religion of peace, reason and morality".
Jefferson assured a Christian religious school that it would receive “the patronage of the government” (Letter of Thomas Jefferson to the Nuns of the Order of St. Ursula at New Orleans on May 15, 1804, original in possession of the New Orleans Parish. )