The way I read the story is that he went to court marshal for disobeying a direct order. After reading the article, he seems very devout in his faith, which I believe is necessary for a minister. However the way the rest of the article reads, it seems like he does things that are a little outside the box for uniformed service.
Last December, the chaplain went on an 18-day hunger strike in front of the White House over the right to invoke Jesus' name outside such services.
As an officer, especially a Chaplin, this is a poor example to set for the rest of the Navy, or any other service. How is the young 19 year old who has been in the service for only a few months supposed to take this, and how will it influence his decisions as to right or wrong. Most young kids would take this as an appropriate action for any grievance they might have in the service because they saw a Lt do it.
The Military is very conscious about where and how the uniform is represented.
The charge centered on a March 30 news conference protesting a Navy policy that requires nondenominational prayers outside of religious services.
The fact that he attended the "press conference" not a worship service, as he stated in uniform is the issue. Unless the article is incorrect, the issue was not that he acted as a Chaplin and worshiped or preached, but that he disobeyed the order to not wear his uniform to a press conference, which displays US Navy support for his cause. A Chaplin in the Navy is not just a minister, but a leader, consoler, mentor, and a crisis management team member. As such there are a limited number that receive this training. We only have 8-10 for my base which has 6000 active duty personnel and their dependants. The Lutheran Chaplin might give his service then give a nondenominational service an hour later. The reason for requiring nondenominational prayers outside a religious service is not to offend another religion. The DoD recognizes most religions from Catholic to muslem to pagan, so I feel that is an appropriate policy ( I certainly don't want to hear a pagan prayer).
My point is that, although this man appears to be a devout Christian, from the example he sets is not becoming of a military member, let alone an officer, and he should probably leave the military quietly so he has a better chance of getting a church to take him.