I too am confused as to why this guy would want to start this group and take the position of chaplain. Like you said, an atheist chaplain is really just a counselor and you already have those. Maybe he is trying to give atheists in the army their own social structure but it honestly sounds as if he is just enjoying the publicity. Almost all atheists I have talked to would agree that it would be ridiculous for them to get together and discuss their lack of belief. It almost sounds as if this guy is trying to be a "leader" for atheists in the army but that contradicts what most atheists stand for which is no atheistic hirearchy. I am suspicious of his motives because he wants to receive the title of "chaplain." I don't see why an organization would be neccessary for an intellectual metaphysical discourse and I don't see the point of his whole endeavor.
Even if the open windows of science at first make us shiver after the cozy indoor warmth of traditional humanizing myths, in the end the fresh air brings vigor, and the great spaces have a splendor of their own - Bertrand Russell