Well, yes. That was the problem with secular authorities being subservient to the church under the era of "Christendom". Secular authorities being in charge without power flowing from the people is worse (communism). That's why we were so lucky to have founding fathers influenced by enlightenment. It corresponds to the free will given to us by our Creator.
And why the US Constitution is viewed as tragic by the Roman Catholic Church to this day.
One can make “at least it isn’t as bad as” arguments and they would be correct. The Inquisition churches seemed to be satisfied if you didn’t stick your neck out opposing them even if you really didn’t believe.
But the problem is fundamental. Governments of secular lands were not in the mission statement of Christendom. Not until the literal return of Christ. The church should have politely declined such opportunities, offering to advise if invited, but never to govern or be viewed as a governing body.
The GOOD that came from the thinking of our Founding Fathers was principally from Christianity ...rather than the enlightenment itself. In actuality, their thinking was a beneficial marriage of faith and reason, with the understanding that both came from God.
“Most intellectual movements are given their name by men who study them. The Enlightenment is peculiar in that it named itself. This happened when certain thinkers and writers, ones who lived and worked mainly in France and England, saw themselves as “enlightened” in comparison with most other men, and, setting out to enlighten the others, said that is what they were doing. Many of the men of whom we speak were trained as mathematicians or scientists. When they spoke of themselves as enlightened, what they meant was that by the light of reason they had freed themselves from ignorance and superstition, which is to say, orthodox religion, and had thereby come to understand that the hierarchically-based, political-social order then prevailing nearly everywhere was bound to be oppressive or downright tyrannical insofar as both those at society’s summit and those lower down in it saw the order as being willed by God.” ...G. Potter
Those who make much of the Enlightenment today are very utilitarian in their views and often call themselves liberals or progressives. They tend to make “reason” (as they understand it) their solitary deity.