There's a flaw in your theory, we've already been told by Index that magic was created by and for people who weren't lucky enough to be born with esper powers. Seeing as this is information coming from the walking library ( or whatever Zell used to call her ) i'd say we can assume it to be true

Actually you know... if you combine that with the history of our own catholic church maybe magic users became Exorcists of the church to purge the demons ( espers ) from the land. That would fit in well with the story and explain the apparent rivalry that comes from both sides.

Obviously now that esper abilities have been analyzed and proven to be natural occurrences by science the fighting has subsided but there may still be members of the church who believe in their own ways and espers who believe themselves entitled to revenge