Too much civil authority over religion.
Maybe I misunderstand your meaning, but that's an odd way of putting it. Most "separationists" argue that religion has too much influence over government, not the other way around.
On the other hand, those in favor of more religion in government often make the claim that Jefferson's "wall" was intended to be "one way", that is, keeping government out of religion. But that just doesn't jibe with the portrait we have of Jefferson. While preventing government from favoring one religious sect at the expense of another was a valid concern, it is clear from Jefferson's writings that it was the corruption of
religion, or more pointedly
the clergy, that he feared would result from organized religions' influence in government and politics.
I would argue strongly that his fears have come to pass, more than he ever could have imagined, i.e., James Dobson, Jerry Falwell, Tim LaHaye, and dozens more, who have allowed their political power and connections to corrupt their own views (and hence their followers' views) of Christianity beyond all recognition.
One more point: People on both sides of the church/state debate need to get over the myth that the Founding Fathers were all of the same mindset and thus unified in their thinking when it came to the Constitution and the role of government. It was no accident that the Constitution is vague in places. They couldn't agree on everything. Which is why we're still arguing about it 200 years later.
In short, neither side can lay claim to knowing the true intentions of the founders, because they were so varied.
Both sides of the debate are right. And both are wrong. Just depends on who you quote from.