"Just another day in paradise," mumbled Mister Waddles, the elderly minister running a broom through his humble parish church slowly. Without warning a thought hit him like a sun bolt from above, akin to those prophets of old. Ponyville was paradise...of a sort.
Was he not by the side of his goddess's daughter? The scriptures had made it clear: When the immortal sun princess was with child, the world's ills would be at an end. Of course, the Nightmare was in the details, namely those original books of faith. Written in old ponish by tribes who'd only just begun cross-cultural exchange, translating this hybrid language to the common tongue had become exceedingly difficult.
'With Child' was a sticking point. The faith could accept Lady Sparkles' form, but her exact origins were controversial.
Still, was she not Slayer of the Night Devil? Chosen of Harmony?
He had faith in Twilight Sparkle.
As long as he doesn't tell her that, it should be fine.
Honestly, Mister Waddles seems a decent sort. He doesn't care that Twilight is a diamond dog and his concerns about her origins seems to be less his own personal opinion and more something that is causing a schism in the faith.
Considering he's fully acknowledging her as the chosen of harmony and the defeater of Nightmare Moon, it's clear he's opted for the pro Twilight faction.
Honestly, it's possible that I could see more progressive branches of the faith like Waddles making a point that the Night Devil and Princess Luna may not the same entity. That Nightmare Moon was a demon that possessed Princess Luna and acted through her body. The fact that the Chosen of Harmony restored Luna rather then banishing Nightmare Moon back to the Moon or destroying her outright could narratively suggest that there was a third party at play.
Not saying the Sisters would enjoy making this possible concession, but if it gets ponies to stop calling Luna a demon who needs to be burned at the stake...