"lawful general order"
How is what he did unlawful?
Because, by offering prayers specific to his denomination at public events where sailors are required to attend (as opposed to denominational worship services, which are voluntary in nature), he is violating the rights of those sailors who do not believe as he does.
Or would you be comfortable with a Muslim chaplain, with a captive audience of sailors that is there under penalty of court-martial, offering Islam-specific prayers?
He got off very lightly.