Any troop for any reason that reuqires a personal bodyguard does not fit into the military organization and can be discharged. The specific reason is irrelevant.

However, if you read the article it was not the fact that he was an atheist that got him in trouble. He's an activist, crusading atheist. He's just pushing HIS religion and got pissed because he was told to stop.

__________________
“The only thing necessary for the triumph of evil is for good men to do nothing” - Edmund Burke

So in the Libyan fable it is told
That once an eagle, stricken with a dart,
Said, when he saw the fashion of the shaft,
“With our own feathers, not by others’ hands,
Are we now smitten.” Æschylus