[PTTG]

You presume the defenses work the same way. Maybe European magic actually did rely on demonic forces, so the divine protection of the Church could overcome it. But ancestral spirits, trickster gods, and other deities are not the same thing as European Demons....

Even if the defenses were fully interchangeable, if the Church successfully purged the native magic users, maintaining a working understanding of countermagic protections for centuries of disuse would be quite difficult.