"our civil rights have no dependance on our religious opinions, any more than our opinions in physics or geometry; that therefore the proscribing any citizen as unworthy the public confidence by laying upon him an incapacity of being called to offices of trust and emolument, unless he profess or renounce this or that religious opinion, is depriving him injuriously of those privileges and advantages to which, in common with his fellow citizens, he has a natural right; that it tends also to corrupt the principles of that very religion it is meant to encourage, by bribing, with a monopoly of worldly honours and emoluments, those who will externally profess and conform to it; that though indeed these are criminal who do not withstand such temptation, yet neither are those innocent who lay the bait in their way; that the opinions of men are not the object of civil government, nor under its jurisdiction; that to suffer the civil magistrate to intrude his powers into the field of opinion and to restrain the profession or propagation of principles on supposition of their ill tendency is a dangerous falacy, which at once destroys all religious liberty, because he being of course judge of that tendency will make his opinions the rule of judgment, and approve or condemn the sentiments of others only as they shall square with or differ from his own"
"You're wrong about Jefferson's "Bill for Religious Rights", it was in fact a warning to the people that aloowing religion and government to conjoin would in fact corrupt both."
The extract from Jefferson's Bill for Religious Freedom that you posted is difficult to read. But I think that Jefferson is actually referencing Clause 3 of Article VI of the Constitution which prohibits religous tests for government officials. Jefferson also seems to be reflecting disdain for the common law system where judges make the law as well as decide cases.
The bottom line is that I question your self-honesty with respect to reading things objectively, particularly when something is difficult to read in the first place. The fact that your "Hollywood" Jefferson probably wasn't warning about keeping religious and state government powers separate is evidenced by Jefferson's letter to Rev. Samuel Miller. Given this letter shows that President Jefferson "passed the buck" for official government recognition of a national religious holiday, "Fasting and Prayer" I believe, from the federal government to the state governments, your idea that Jefferson meant to warn against cojoining religious and government powers doesn't hold water, particularly with respect to the state governments.
"I consider the government of the United States as interdicted by the Constitution from intermeddling with religious institutions, their doctrines, discipline, or exercises. This results not only from the provision that no law shall be made respecting the establishment or free exercise of religion, but from that also which reserves to the states the powers not delegated to the United States. Certainly, no power to prescribe any religious exercise or to assume authority in religious discipline has been delegated to the General Government. It must then rest with the states, as far as it can be in any human authority." --Thomas Jefferson to Samuel Miller, 1808. http://tinyurl.com/nkdu7
Jefferson also reflected on the 10th A. powers of the states to address religious issues by noting that the states were trusted with the care of our religious freedoms.
"Our citizens have wisely formed themselves into one nation as to others and several States as among themselves. To the united nation belong our external and mutual relations; to each State, severally, the care of our persons, our property, our reputation and religious freedom." --Thomas Jefferson: To Rhode Island Assembly, 1801. ME 10:262 http://tinyurl.com/onx4j