The problem...
The problem with HRE, which manages to be more centralized and unified, is that at that time political opposition and religious dissent, were for everyone, interchangeable terms together.
The centripetal forces that fought to modernize it and make it a condition, the style of the other European States of their time, were at this time the Habsburg and instead centrifugal forces were represented by the powers Reformist internal (German) or external.
Even though this causes the cultural instinctive rejection in many people whose cultural traditions were marked by the survival of the Reformers
who managed to maintain and justify ideologically, through its religion their political autonomy and taxation traditional privileges of feudal origin.
Obviously the intervention of France, was motivated to prevent the emergence of a great state, ruled by the Habsburgs his enemies who surround to France.
But if what you want is a non-Catholic HRE, should prevent a member of the Habsburg family can become Emperor and perhaps replaced by a member of a noble family that could be more feasible to convert to the Reformed faith or too weak to oppose her, but in the latter case would also too weak to even attempt to centralize and unify the empire, facing his fellow Catholics already.