Border gore is just the way things used to be. My more OOC trouble with accepting the Rhine is that it's Catholic majority which changes important dynamics in Prussia. Kulturkampf, for example. Thr other is that I wanted Ptussia to be weak enough for Saxony to influence them more.

If border gore is a concern we can just list non-Austria and non-Prussia as the German Confederation. Rhine itself may be part of an even tighter confederation of small states of which some are Prussian territories.

If I must take Rhine tho, I can manage. It'd be ugly but with the magic of narrative control it is possible things develop towards religious freedom. Well, more of a religious cold war where Saxony keeps their faith, Prussia keeps their faith and the Rhine is also left alone. All the while they are under one ruler. 
But you can see how this all would lead to me dedicate way too much effort into pacifying/subjugating religions and not everything else. Which is why I am so vonflicted on this.