The Duchy of Masovia was in the middle of Poland and included Warsaw. I doubt Prussia would annex it. Silesia was annexed for wholly different reasons, and the partitions happened because of the political system of Poland and three enemies on all sides. I doubt Masovia being Protestant would change that, since it'd still be ethnically Polish.
Nitpick: OTL Prussia annexed Warsaw and northern Masovia in the third partition. It was call Neue Ost-Preussen IIRC.
Anyway, it is dobtful that the Masovian Piasts surviving and converting to Protestantism would affect the general population. While there was a significant Lutheran movement there at some point, Poland was one of those countries were Counter-Reformation in fact worked very well - in part thanks to the Swedes who made it quite visible that the Protestants were
really into religous warfare when Poland had been employing tolerance.
So I doubt it would be possible. If the Prussians annexed it - well, they didn't convert Greater Poland OTL. If the Masovian Piasts converted - hard for this to lead to the general population converting
en masse. If religous tolerance was abolished - the country would be even more Catholic.
I suppose your best chance would be for the Masovian Piasts to live on, become elected at some point after the Commonwealth was founded (maybe in exchange for Henry of Valois, Bathory or the Vasa's - any would do) and thus prevent wars with Sweden somehow. With the nobility converting to Lutheranism and Calvinism, they may very well start migrating to cities to start merchant businesses there, creating a situation where Masovia would have a Catholic rural area and Protestant cities bustling with trade - especially those along the Vistula, sending and receiving stuff through that route.