In particular, Michael Weinstein was upset that the Academy Superintendent, Vice Admiral Jeffrey Fowler, had issued an order that the ceremony stop, only to later allow it to continue. In criticizing the reversal, Weinstein said, in typical fashion,
Vice Admiral Fowler…wins the ‘Fundamentalist Christian Most Intimidated Award’ for 2008…Such profound duplicity and cowardice fatally disgraces the U.S. Naval Academy…
The implication in the article is that the Vice Admiral had his order overruled. (Given that the article also says the Admiral would refuse to return if not “obeyed,” which is an unusual thing for an officer giving an order to say, it is possible that an “order” was not given, but that he expressed a preference that is being misreported.)
It might be somewhat ironic that Weinstein, who founded the Military Religious Freedom Foundation (MRFF), would back a military officer who attempted to dictate the rituals of a religious chapel service. That very issue–that a state actor would direct a subordinate’s religious observance–was probably what led to the reversal, as such an order would be unConstitutional.
Also reported on Reasoned Audacity.