I have seen a civil war once in the mod, and it happened to the Venetians. Generally, civil wars happen only to large factions with plenty of lands. I do not think you can ever get a civil war as the Moldovan principality unless you expand a lot. I think the reason we see less civil wars in Pike and Musket is due to the good balance of the game - it is harder for factions to grab plenty of lands and make a great expansion. Also, in the vanilla game many factions are prone to excommunication. In the mod, this does not apply to the protestant factions, and the catholics are either all roughly the same size (the various Italian minor factions) or simply preoccupied attacking Muslims and Orthodox.