In fact, the generals whom Mikey thought would face a reckoning under a Democratic administration remain in place or in line for promotion. Not only did Obama keep on Robert Gates as defense secretary; he retained the secretary of the Army, Pete Geren—another star of the Christian Embassy video, who also, in commencement remarks at West Point last year, characterized America’s wars in Iraq and Afghanistan as struggles for religious freedom against the “darkness and oppression” of radical Islam—and also appointed as his national security adviser the retired Marine general James Jones, a regular on the prayer breakfast circuit. Nobody believes the new president shares Bush’s religious sentiments, but clearly he is willing to shave constitutional protections in exchange for evangelical peace. The new president appears to have adopted a hands-off approach not just to religion in the military but to the very relationship between church and state.
The Pete Geren example is weakened somewhat, but the weight of the rest of the article (it's a long read, but very worth it) bears down and makes that paragraph almost crushingly disheartening. I can't recommend strongly enough that you go read the whole thing.