I discovered the CIA chaplaincy service while doing research on a human right case the CIA (and the US) lost. It seems the CIA had arrested a "suspect:" and, for four months, beat him, tortured him and sodomized him - only to discover it was a case of mistaken identity. So they shackled him, blindfolded him, then took him to another country, and dumped him by a roadside.
So how do you feel about the CIA having chaplains? I can see the case for it. a tired agent after a day of beating, torturing and sodomizing could well benefit from a few words of comfort, and some reflection.