I read Daniel Dreisbach's Thomas Jefferson and the Wall of Separation between Church and State over the last few days. The book is a storehouse of information related to Jefferson's metaphor in his letter to Danbury Baptists about the first amendment "building a wall of separation between church and state." The author, however, has little regard for the metaphor as a principle of jurisprudence and he demonstrates an eagerness to offer strained interpretations of the material to discredit the principle.
A prime example of this straining is found in his explanations of Jefferson's opposition to Thanksgiving day proclamations. As President, Jefferson refused to designate days for public fasting, thanksgiving, and prayer as had his predecessors in office, Washington and Adams. Jefferson initially understood his letter to the Danbury Baptists to be an opportunity to publicly explain his opposition to governments prescribing acts of religious piety. Language to that effect was prominent in the first draft of the letter to Danbury Baptists.
On the recommendation of his Attorney General, Levi Lincoln, Jefferson removed a sentence that identified proclamations of fasts and thanksgivings with the practices of "the Executive of another nation as the legal head of the church," i.e. by the despised English King George III. Lincoln advised him that performances of religious devotion were "venerable" practices both in his own Republican party and in the opposition Federalist party. Jefferson removed that sentence for political reasons -- not because he had a change of heart.
Dreisbach does his best to make it appear that Jefferson's opinion about governments issuing proclamations for "performances of devotion" was ambiguous. He cites proclamations that Jefferson signed while governor of Virginia as proof that Jefferson approved the mandating of religious exercises by state magistrates. Proclamations and Notices that Jefferson signed while Virginia was under English rule (1774), however, hardly serves as credible evidence for what Jefferson believed proper for the governing of states in a new nation. Proclamations that he signed as Virginia's Governor after independence (1779), but before the legislature had enacted his Bill for Establishing Religious Freedom (submitted in 1779, enacted in 1785), are equally suspect.
In reality, after the Constitution and First Amendment were passed (1789), Jefferson's first draft of his letter to Danbury Baptists (1802) is the best evidence we have of Jefferson's deepest convictions about the proper relation between religion and government. He believed the First Amendment prohibited the President and Congress from any action that would establish religion and its practices. He hoped his letter would "sow useful truths & principles among the people, which might germinate and become rooted among their political tenents."
If Dreisbach were merely insisting that Jefferson was an advocate for states rights and that he understood the Constitution to apply only to the federal government and not to the states, he would merely be restating an undisputed truth. Dreisbach is suggesting more. He's trying to leave the impression that Jefferson advocated for the establishment of religion by the states -- which he most certainly did not. On the contrary, he was planting seeds that he hoped would encourage disestablishment of all the colonial establishments of churches. By 1833 his seeds had born fruit and all of the states had disestablished their churches.
To understand Jefferson's deepest convictions about separation of church and state, all you have to do is look at the legislation he authored for Virginia after the war for independence. It was a Bill for Establishing Religious Freedom -- not for establishing a state church. That bill along with his authoring the Declaration of Independence and the founding of Virginia College comprise the legacy for which he was most proud and wanted to be remembered.