No religion or belief system has any special card to avoid being erroneously characterized or presented cluelessly in an anime.
The Japanese simply love to take elements from other cultures and splash them about in their entertainment. That's how we get sexy nuns, Santa on a crucifix, that opening credits moment in Kemeko DX, incredibly wierd re-interpretations of Shinto or Buddhist elements, etc.
I don't see any reason any religion (or non-religion) should be exempt.
The civil response is "Zoinks, that was silly...".