I think Ranni's questline is implicitly a redemption arc for her. That is she's very upfront with the belief that faith and love are lies and she intends to rid the world of them. By the end of the questline and into her ending, her tone has changed considerably, between Iji's and Blaid's services and sacrifices and the journey the Tarnished has endured. She flat out says in her "parting words" to tell the former that she loves them, and the Tarnish all but goes through a marriage ceremony with her by the end.

The Age of Stars ending doesn't seem like an "upending" so much as a peaceful transition to a new era.

Was Ranni a villain? Yes. Was she one by the end of her questline? I would say no.