I think you've misjudged me. To address your concerns, I'm not upset about the Christian content in early American schools. I was questioning Jefferson's (that is, the federal government's) involvement.
I understand that, sorry if I came accross as otherwise.
It's not so much that the Federal government was actively involved with Christianity and public schools, it was more like the school teachers, administrators and society in general were practicing Christians, and viewing Christian morals and principles as healthy for our country the government simply remained silent and let it be. My impression is that "the government" back in those times was much more intertwined with 'we-the-people', and vise versa. Bear in mind that back then people still (rightly) believed that all civilized law derived from the Ten Commandments, and that it was therefore impossible to separate the two. So I would say the schools taught Christian morals, values and principles, but not actual theology.
All this widespread objection to prayer in public schools and the suppression of Christian symbols on public property is a fairly new phenomenon, in any case.