My understanding is he has a problem praying as he wants to by saying in Jesus Name; however, he's probably gone about this the wrong way.
Having said that, I've always found the chaplain service a bit silly. Having a Catholic priest pray for a muslim on his deathbed because there isn't an imam available...is just stupid.
The more of a devout believer you are the more silly it is to have another faith "bless" you on your way out of the world.
The best answer is to let catholics teach catholics/protestants preach to protestants/mulims to muslims/etc...
Then just hire the correct number based the number of military members that subscribe to that faith. If we dont' have your faith...sorry choose a more mainstream religion or learn to practice on your own.
One issue this guy is talking about is that he's not allowed to pray "In Jesus Name"...it has to be a generic prayer at community events. So that does bring up a sticky situation. I always prayed in Jesus Name, but what would I think if I was a banquet and the Priest prayed through Mary? Or a Muslim prayed to Allah.
Believe it or not, but no priest is going to offer a prayer to Mary at a mixed gathering. Did you know that at mass,she is mentioned only twice. Once in ther Nicene Creed, and later as chief among the saints. As for Allah, that is simply the Arab word for God.