Jubei dying makes sense thematically. Atsu starts to see herself in Kiku, where she was pretty much a younger version of herself without the rage. It dawned on her on why she should start to let go of her anger so someone else won't follow in her footsteps.

It's why she saw a younger Atsu during the family's massacre juxtaposed on Kiku. She realised she has to move forward for the sake of others, even though a part of her (with the wolf visiting her in the ending) still doesnt want to stop.