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For whatever he meant he certainly did not intend for religion or religious themes to be expunged from public environs. If this was so he'd have voiced an opinion on it. He, or even any of the Constitution's framers, seemed to have had any objections to religious displays, or the Bible being present at public functions.
His main objection arose from the way the British Anglican Church wielded it's authority in the colonies prior to the Revolutionary War., although Mr. J wasn't either too pleased with some priests and bishops he encountered in Catholic France who more or less led their flocks more from tyranny than brotherly love.

TJ most assuredly believed in God, i.e., the God of Moses. Where he had doubts, I believe, was in man's behavior towards God and His laws.

Is it any wonder our nation's two greatest Presidents were lovers of the land, (and horses), who chose to live on mountaintops.

Thomas Jefferson did not intend for religion or religious themes to be expunged from public environs.

Senate Chaplain Episcopal Bishop Thomas John Claggett believed that the election of Thomas Jefferson in 1800 was the triumph of Jacobianism and he expected President Jefferson to preside over a transformation to the French system by implementing a reign of terror and then abolishing religion.

For whatever Thomas Jefferson meant he certainly did not intend for religion or religious themes to be expunged from public environs.

What he wanted expunged was civil authority over the things of God, such as the illegally assumed Presidential authority to issue religious recommendations.

If this was so he'd have voiced an opinion on it. He, or even any of the Constitution's framers, seemed to have had any objections to religious displays

What religious displays did they have no objection to? I didn't know the federal government set up religious displays during the early years of the republic.