While reporter Alan Cooperman (whose pieces on religion I generally find fair) catches almost everything, he doesnt note this important proviso in the guidelines:
[T]here may be extraordinary circumstances where the potential benefits [of prayer] for the welfare of the
command outweigh the potential of causing discomfort. These circumstances might include mass
casualties, preparation for imminent combat, and natural disasters.
He also doesnt note that the guidelines permit a moment of silence on routine occasions.
In general, the guidelines, which apply now only to the Air Force but may be extended to all the services, strike me as a commonsensical response to religious pluralism, urging accommodation of the religious needs of servicemen and women, placing national service and solidarity at the forefront of everyones concerns, and reminding officers that the hierarchical (I use this word self-consciously) nature of military service gives officers a special responsibility to avoid confusing their subordinates. These, by the way, are not the guidelines issued by a "theocracy."