Huh. Permanently deciding the religious nature of the Holy Roman Empire in a single war seems a bit... odd, considering how many cycles of fighting in took in history. If, as is claimed, it's supposed to represent all the religious wars in the Empire, it ought to go on longer- perhaps allow defeated religions to try again for a few times. And I agree that it seems a bit "rail-roady". At the start, why should the Emperor automatically loose his status on converting? He's been elected, he has the apparatus of government (to the extent there is one)- if people want to depose him for his religion, they should have to fight to make him step down. And reformed comes off very badly here. Suppose the majority of states in the Empire go reformed (unlikely, but not utterly impossible). They have no way of obtaining rights except by backing a Protestant rebellion- and if they win rather than white peace, they're still out of things. I can see cases where this would really be worse than what we have now, forcing the game's history into paths that are complete nonsense in their own terms as well as unlike our history.
Fighting the league headed by the Emperor to change the HRE's primary religion and fighting another war to then unseat the Emperor sounds a bit redundant. If you've made the HRE Protestant, you've already beaten the Emperor decisively.