If we really want to dive into history, the Protestant league should dismantle the emperor's unions and maybe put France on the throne if they win, while a catholic victory should end the reformation and convert all heresies right back to Catholic. Just because. All of this ignores the historical reality that the 30 years war was fought primarily between two catholic nations using religion as a pretext. The religious side of the peace has little to nothing to do with the centralization of the empire, which was arguably far more disturbed by the ruling dynasty having the majority of its power base outside the HRE, than by some trumped-up belief system.
If you REALLY care about making the HRE model history better for no good gameplay reason, reforms should have a long cooldown (maybe 15 years, or 1 per emperor's lifetime), Bohemia needs to lose its ludicrous imperial authority bonus (it was an elector that couldn't even participate in many imperial functions; it was an autonomous monarchy not an imperial prince) and you should lose IA monthly if less than 3 electors are a theocracy. Or, you know, not make the HRE be 100% bonus in every way until the end, so that leaving it has no merit and the only reason to not want to be in the empire is because it's slowing down your blobbing?
Frankly, I think the current HRE system is actually ideal to be dropped, as-is, right onto France. The actual Holy Roman Empire needs a full rework!