I have heard the soundbite. I believe her contention was that the phrase "separation of church and state" is not in the Constitution...and indeed it isn't. I do not think after hearing it that she was surprised that the concept exists, only that she disagrees with the interpretation. As you all know, the phrase came from a letter from from Jefferson to a church to assure them that the government would not be interfering with them.
From Wikipedia (not my favorite source, but the quickest one to find) -
Quote:
The separation of church and state is a legal and political principle derived from various documents of several of the Founders of the United States. The First Amendment to the United States Constitution reads "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof . . ." The modern concept is often credited to the writings of English philosopher John Locke, but the phrase "separation of church and state" is generally traced to an 1802 letter by Thomas Jefferson to the Danbury Baptists, where Jefferson spoke of the combined effect of the Establishment Clause and the Free Exercise Clause of the First Amendment. His purpose in this letter was to assuage the fears of the Danbury, Connecticut Baptists, and so he told them that this wall had been erected to protect them. The metaphor was intended, as The U.S. Supreme Court has currently interpreted it since 1947, to mean that religion and government must stay separate for the benefit of both, including the idea that the government must not impose religion on Americans nor create any law requiring it. It has since been in several opinions handed down by the United States Supreme Court, though the Court has not always fully embraced the principle.
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While that is the currently accepted phrase, it isn't in the Constitution. I honestly don't think she was shocked about the principle coming from there, but that she was pointing out that those words do not exist in the document. It could be that people here find that more concerning than her supposed ignorance.