I'm not sure. The Thirty Years War as it unfolded was a result of something other than generalized religious and political issues.
Maybe it wouldn't unfold the same way, but a war was inevitable. There was the problem of Calvinism not being legal in the HRE, France wanting to regain the position it lost because of the Religious civil wars, the Spanish and the Dutch were bound to go head to head after the truce expired. Not to mention the issues of Denmark and Sweden. The war might not start in the same place or same time but these issues were bound to come to a head eventually.