Read some of these articles to get a feel for what happens (apparently) too frequently in the military: Military Religious Freedom Foundation.
Let's get this out there first: Soldiers have the right to worship or not worship whoever and whatever they like. The Military, and the nation as a whole, has a responsibility to look after the psychological well-being of the soldiers it employs. Our nation has no national faith, and our constitution does not endorse any religion (it does the opposite). The first duty of every soldier is to protect the state and the constitution that comprise it.
I haven't been able to find all the articles I've read about this - but in this instance I understand that the soldiers were forced to do the deep-cleaning busy-work that is normally reserved as a punishment (or encouragement) for those who underperform. I also believe that the general responsible for this program was reassigned to a minor post after all this came to light. And, as usual, I'll mention that the MRFF usually acts on behalf of christian soldiers who don't happen to be evangelical. But I'm sure that soldiers often must deal with all kinds of peer pressure with regards to their beliefs and personal preferences (say, involving drinking or sex).
So, why do I say that the military needs us? Because it damn well does. It seems that the military does not offer much (comparatively) for the atheists and agnostics or people who don't believe in mainstream religions. Anecdotes point to a military establishment that gets much of its public support and policy influence from the religious right (that small and potent group of evangelicals). At least 15% of the American public is faithless, and we should be doing our part to make sure the military, or any other public institution, isn't co-opted inappropriately, in a manner contrary to the principles of personal freedom and separation of church and state, by any organization - religious or otherwise.
If anyone reads this who could offer more information or numbers on these programs and behaviors (I'm looking through public budgets and the like, but I don't have a tremendous amount of time for deep research into the matter), I would love to hear from you. Also, anyone who could suggest things that secular soldiers might want would be appreciated (not sure how much I can do, but I can try to start the ball rolling).