"What he wanted expunged was civil authority over the things of God, such as the illegally assumed Presidential authority to issue religious recommendations."
You still need to make a distinction between federal and state governments where civil authority is concerned as Jefferson did. The problem is that the people have forgotten that the Founders wrote the 1st and 10th Amendments in part to reserve government power to address religious issues uniquely to the state governments. Secular judges are consequently walking all over our religious freedoms because of this ignorance concerning the 10th A.
I agree. And for curiosity's sake, what do you mean by "recommendations"?
As an aside, I believe TJ would be greatly appalled at how the phrase separation of Church and State has been twisted and misappropriated to fit the ideology of many on the Left and some on the Right.