So, we should just accept backwards superstition and archaic societal ideals because Bavaria is made up of Christian reactionaries?

Enforce it from Berlin then. Deploy personnel to monitor the application. If Bavaria tries to play favorites, big fines for each case.

While i agree with your sentiment the reality is that christian fundamentalists (in appearance, in behaviour they are devilish unchristian) are still powerful in German politics and we see a resurgence in their popularity among the voters. The majority of the German people is happy with persecution of muslims and doesnt care about favoritism towards christians.