Thomas Jefferson was no secularist

Regardless of how high one thinks Jefferson's wall of separation of church and state should be construed, one point that many modern commentators of a secular bent overlook is that Jefferson was consistent to emphasize not just limits on religion's power to use state power but also on limits of the state's power to force people to violate their sincerely formed religious consciences. As he wrote in the Statute of Virginia for Religious Freedom:

Well aware that the opinions and belief of men depend not on their own will, but follow involuntarily the evidence proposed to their minds; that Almighty God hath created the mind free, and manifested his supreme will that free it shall remain by making it altogether insusceptible of restraint; that all attempts to influence it by temporal punishments, or burthens, or by civil incapacitations, tend only to beget habits of hypocrisy and meanness, and are a departure from the plan of the holy author of our religion, who being lord both of body and mind, yet chose not to propagate it by coercions on either, as was in his Almighty power to do, but to extend it by its influence on reason alone[.]

Note here that the justification for this approach to limiting state power over religion and religious controversies is in God's own act of creation of the human mind, and God's will for human beings to be free in matters of religion. In other words, Jefferson's commitment to religious liberty sprang from his own theological beliefs about God's will and how God seeks to execute his purposes in human life. His contention is not secular at all, it is profoundly religious and profoundly theological.  And it parallels his long-standing views on the matters of religious liberty that he set out in his Notes on Virginia, where he writes the famous statement:

The rights of conscience were never submitted, we could not submit. We are answerable for them to our God. The legitimate powers of government extend to such acts only as are injurious to others. But it does me no injury for my neighbour to say there are twenty gods, or no god. It neither picks my pocket nor breaks my leg.

Note again the root justification for Jefferson's views here.  Human beings cannot rightly submit their conscience to the state because our consciences do not come from the state nor can the state properly judge out consciences. The judgment of our consciences is left to God, a God that Jefferson claims as his own.

Thomas Jefferson's views on the limits of state power in religion themselves reflect an attempt to use the agencies of the state to promulgate a theological view of the human person and God's purpose in creating that person. His approach is not secular. It is sacred.