My theory is a simple one, some scholars believe that originally the teachings of Mephala were actually that of Hermaeus Mora this can be furthered by the Morag Tong's name, I believe the Morag Tong were once the Foresters of the forbidden or knowledge forest (We have yet to determine what Hermaeus means but Forbidden or Knowledge both sound suitable for him)
I believe the Morag Tong were once a order of scholars who sought out all things forbidden and guessing by that they had to remain in the shadows which might also explain how Mephala managed to become one of the Good Daedra. Somehow the Morag Tong lost their way of knowledge and instead found the way of espionage and assassination.