What I think (is probably wrong) Lois sides with her father and urges Superman to see that kryptonians are too dangerous. This is foreshadowed by Lucy's death and mirabi's cosplaying Supergirl taking down Mon-El on national TV. Lois totally buys it.
Superman who already has sided with Lois once despite the fact he didn't agree with her about Kara finally takes a stand about Lois' bile. She'll see that as siding with Krypton.
Superman is trapped in the middle but must side with Alura because Earth turns against him. Supergirl stays with her mother and sides with Krypton after Lane's actions and Cat Grant's headlines.
We'll see Superman vs earth without compromising his character.