Likewise, Jefferson did not construct a "wall of separation", Justice Hugo Black did that in Everson in 1946. In fact Jefferson and Madison authored a law, while members of the Virginia Legislature, proscribing penalties for breaking the Sabbath. Jefferson, as POTUS, used the public treasury to build Catholic missions for the Indians and man them with the word of God, the Bible.
And that's the rest of the story.
A resolution calling for a national day of Prayer:
RESOLVED, That a joint committee of both Houses be directed to wait upon the President of the United States, to request that he would recommend to the people of the United States a day of public thanksgiving and prayer, to be observed by acknowledging, with grateful hearts, that many signal favors of almighty God, especially by affording them the opportunity peaceably to establish a Constitution of government for their safety and happiness.
US Congress, 25 Sep 1789
These historical points are interesting, but the overall point -- and one of the key points of the original article -- is that separation of church and state is essential to a free society. Jefferson and Madison were absolutely correct on this point. We have the benefit of more than 5,000 years of human history to illustrate the consequences of people who try to impose their particular religion on the rest of us. We saw it in spades during the Dark and Middle Ages, the heyday of religious rule. We see it today in places like Iran and Saudi Arabia, as well as in the Islamofascist terrorist movement. In sum, theocracy and religious fanaticism, in all of their forms, is hazardous to human life and well-being.