It's not really settled law as to if something like "so help me, God" is an Establishment Clause violation. Of course, on the flip side, it's not settled law that it isn't, either. Justice O'Connor, in a 2004 concurring opinion (i.e. not the holding of the Court), noted some examples of use of "God" in ceremonies that don't, necessarily, mandate a belief in a deity. The Marshall of the Supreme Court, for instance, says "God save the United States and this honorable Court," and "In God We Trust" is printed on our money. Witnesses sworn to testify in Court are asked to tell the truth "so help [them,] God."
I don't like to use so-called "originalist" arguments for interpretation too much (as, in many cases, it results in absurdity); however, phrases like "so help me, God" were around at the time of the ratification of the Constitution and have been in use many years since then. Justice O'Connor's point-and she was a moderate pragmatist in her judicial philosophy-was that it lacks significant meaning, in itself, as a religious affirmation, and is around now in what amounts to a vestigial sense. It would seem that it would thus not be too big a deal to get rid of it, but its current existence, at least according to her interpretation, doesn't rise to the level of a First Amendment violation.
If I'm honest, I can see your point to the contrary, and I'm not sure that I side with the retired Justice. Certainly, I don't agree that the removal of the phrase from a government oath constitutes some war on Christianity (or any other religious sect).
For what it's worth, I identify as atheist as well.