It could work. I wonder if, perhaps, they could replace vanilla heresies with dogmas based on certain church ideas. Transubstantiation, the holy trinity, icons, priest celibacy, etc. Different church figures over time will generate different views. High religious authority, they will tend to stay consistent, low religious authority, the spectrum of "acceptable" will drift until a full-blown heresy appears. It can either be adopted by characters or snuffed out from there, forming a full-fledged church when an independent ruler king tier or higher adopts it. Or a church council is called to decide. Add in characters trying to change prevailing opinion, anti-popes who have their own slightly different agendas, you have a religious landscape that at the very least would better simulate what heresies were. Could even work with mending the schism—resurgent Byzantium could start causing Catholics to shift more organically, before the full-blown unification with the fall of Rome.