So long as people with a religious opinion and/or outlook are involved in government, there will be arguments about how much of the former the latter has. There is always going to be a problem about where to draw that line - and I know I'm not telling you something you don't already know!
My full, unfettered opinion about it is that I think it is wrong to leave "under God" in the official PoA because any attempt to enforce a religious POV is doomed to failure. Instead, I think a religious society should build up from the bottom: e.g. a country is Christian because that's how the people willingly live, not because the laws have that slant. The un-religious and a-religious should not be targets for religious enforcement.
I also don't think you can ever fully separate church and state: even the abscence of religion can be regarded as a religion.
Wade.