Seeing as how the love of moneyis the root of all evil, we may as well have some idolatrous god or goddess on the coins. At least that way, we would honestly acknowledge our pagan worship of materialism.
Getting back to separation of church and state, however....
Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof.
the "God" on the money is an unknown god, in my opinion.