I read the article earlier before coming to BB and he has been diagnosed with depression. He admits that it played a part in his decision. It is good he made this decision now and not later.
That said, since West Point just had their first gay marriage I find his argument ironic, if not absurd. The military goes to great lengths to meet the spiritual needs of all troops. There is nothing religious about asking people to be quiet and respectful while others pray. Also, chaplains have been told to not pray according to their personal faiths but told to take a more universal pantheistic bent.
Religion in the military has really become a tradition issue, not a real faith issue, as far as policy is concerned.