This would be a TWO PARTER episode
100 years ago, a scientist pony discovered a shocking secret about Princess Celestia, believing her to be a fraud, and feeling Friendship and Magic were not all that they were cracked up to be.
As a result, he was put on trial, scorned by the villagers and believers in friendship and magic, which began a great debauchery in all of Equestrian history, that it nearly drove everyone into chaos over their beliefs.
LESSONS:
1: Don't let others tell you how to think or what to believe in or worship.
2: ONE WAY... is not the ONLY WAY.