This is one of those stories where I think there's probably a lot more to the story. Sorry, but these "I'm being persecuted" stories never seem to pan out the way they're originally reported.
Here's what makes me wonder:
He says he got in hot water during the summer of 2004 while aboard the USS Anzio for preaching an evangelistic sermon at the funeral of a Catholic sailor in a base chapel. The lieutenant said he was reprimanded by two senior chaplains and, in March, sent ashore to Norfolk.
What, precisely, did he say in his sermon? Perhaps the senior chaplains had a legitimate complaint -- perhaps Lt. Klingenschmitt was bashing Catholics, for example (something that is not unheard-of among ardent evangelical protestants) -- in which case he deserved to be reprimanded.
I've learned to distrust stories like this. I suspect that Lt. Klingenschmitt is not as innocent as he makes himself out to be.