Given that religious wars helped cripple Habsburg efforts to centralize Germany, I'm not sure how this would help.
We should first keep in mind that religious conflict in the early modern era both were problematic to England and France as countries and were boons to monarchical institutions. In the former, the English Reformation allowed Henry to centralize and personalize the government. Later and on the other side, Louis XIV used the rationale of fighting Protestants to justify wars that would further his imperial ambitions.
I think in the context of the sixteenth century, the antipathy of Protestants and Catholics doesn't help (it in fact hurts) the process because it places the most viable central institution (the Holy Roman Emperor) on the side of the Catholic Habsburgs, whose power centers (Bohemia, Moravia, Silesia, the Spanish Netherlands, virtually all their lands but Austria, in fact) on lands that are peripheral and non-German, whereas the meat and sinew of what would have to become any German state was in the hands of the Protestant princes (Brandenburg, Saxony, Palatinate, Hesse).
So the Catholic Holy Roman Emperor and the Protestant princes spent the sixteenth century circling each other like great cats, knowing exactly what would happen if they failed to come to a liveable arrangement, and living in a world that still hadn't formulated any conception of the separation of church and state or even freedom of conscience, which made it all the more difficult.
In our history this resolves itself ultimately when the German states become absorbed into a Protestant kingdom (the Prussians), with the Habsburgs forming their own superstate out of their lands and the spoils of their wars with the Ottomans.
So I think to unify Germany in the sixteenth century, you somehow accelerate that basic process.
That's why in my idea I nominate the Saxon Electors of the sixteenth century for the job of building the nucleus that in our timeline Prussia became--lumbering, portly and quarrelsome as they were (seriously--clicking through their pics in chronological order on Wikipedia is like watching the evolution of the ship captains in the portraits in Wall-E).