Varis will probably aid us and then likely be killed. I don't see him joining us, but it's a common trope in Japanese media (anime/video games) where a Season 1 boss ends up joining forces with the protagonist because an even greater evil arises that threatens them both or the world. Varis wanted to expand his empire to bring about security for his people and enlightenment/science for others, while quelling barbaric primal practices. He was indifferent towards how Ala Mhigans and Domans were treated and let his Legati each handle their own affairs unhindered. Gaius ruled with an iron fist but he was merciful, level-headed, and fair. He didn't slaughter or enslave civilians. Meanwhile, Zenos enjoyed treating Domans like cattle and doing whatever he wanted to them. Varis was complicit but he did not outright order anyone to mistreat anyone.

There might be a problem when with Varis' help we destroy Solus with the Sword of Light and that tips the balance so far to light that we trigger the flood.