I am pretty sure they aren't using them to grade anyone. The military here has pretty stringent policies in regards to religion invading anything. They keep the chaplaincy itself in check quite a bit.
In itself, the chaplaincy is an extremely interesting inter-faith organization. The men and women within its ranks have to find a balance between their ministry and their service to country, as defined by their motto "Pro Deo Et Patria". They work with soldiers within their own faiths and without, providing counseling as well as religious services. They are NOT, EVER, permitted to proselytize. Doing so prevents promotion and can lead to lost jobs. If you want to preach, the military is NOT the place to do so.
Air Force Academy turning into a seminary? That sounds odd and something more do to funding, but I don't know anything about it. It wouldn't be the Air Force Academy if it was a seminary. A seminary has to be backed by ONE religious affiliation. I mean, which one were they trying to pick?
They ask these questions about soldiers' financial health, domestic lives, and other very invasive things too. Religion is the only one that seems to get anyone riled up.
With all the issues that crop up daily with soldiers, anything preventative that shows them where they can go (or maybe shows a buddy where to send them) isn't a bad thing, IMO. That's from the perspective of someone who is thinking of people who are hurting rather than people who are happy.
If you are happy, you would say that you were comfortable with your spirituality. Being atheist doesn't mean, to me at least, that you aren't spiritual. It just means you don't believe in God.
I'm more offended by this guy's implication that an atheist isn't a) spiritually complete, and b) has no purpose in life.