Not really. If the Habsburg had gone Protestants (but you need someone different from the King of Spain Karl V, as his younger and Spanish educated brother Ferdinand was more willing than him to deal/compromise with Lutherans instead of destroying them) is highly likely who the whole Holy Roman Empire would have become either Protestant or secularized and in any case the Imperial election for the Habsburg would not be in danger as they had the Bohemian vote who was the deciding one (as three of the other six were in the hands of Catholics archbishops and the remaining three were of the rulers of Brandeburg, Palatinate and Saxony who were all Protestants).Due to being the Holy Roman Empire the Habsburgs had to keep Catholicism, converting to Protestantism would undermine their claim to the HRE. They also enforced Catholicism in areas where it was somewhat counterproductive like the border of Hungary with the Ottomans