Gene Roddenberry, raised as a southern baptist, was agnostic in his adult life. If i remember correctly, i read that Roddenberry predicted religion would be extinct in the future and hence no Chaplin on star trek vessels in his version of the future. Maybe the nearest thing was the very secular Counselor Deanna Troi.
If you really want a religious type of Counselor, i would go for the snake handlers of the Pentecostal denomination. I would love to see the Chaplin handling a snake in the background while Picard negotiates with the Cardassians.