Well, first of all because those followers/worshipers never went anywhere. If their thing is making strange dances in the aurora, and because they do that their tundra resources provide them with more culture/faith/whatnot then why should that change just because some nutjob decided to start a new cult in a city 40 miles away.
I can see them getting converted or at least partially converted to the new religion instantly, but I just can't see them randomly disappearing.
But the old faith (the pantheon) shouldn't contribute faith towards a missionary for a new faith you just founded, at least not logically.
We're gonna try the 'pantheons go away' model for fun with this version. We'll see how it goes.