That must be from the book Keith didn’t get to work on, that most Eberron fans consider non-canonical because of how badly it gets a ton of stuff wrong.
The Purge happened in what is now the Kingdom of Aundair, and parts of the Eldeen, not across the continent, and it wasn’t an action taken by the whole Church.
The Aundiarian Pure Flame zealots are the spiritual (and often literal) descendants of the wayward zealots who commutes the atrocities of the purge.
Also in every other source IIRC, the purge exclusively target lycanthropes, not shifters. Shifters got targeted by individual Templars and overzealous communities, not by the actual mandate of the Church.