I would think season 2 would be mostly about Ahsoka and Sabine on Peridea with Baylan and Shin and not show anything about Thrawn, Hera, or what's going on back home. I would think they would save Thrawn for the big Ahsoka 'Avengers' style movie when Ahsoka, Sabine, Huyang return.
With Ahsoka, Sabine, Huyang on Peridea you could craft a lot of stories of them possibly making a treaty with Baylan and Shin to get off the planet and back to their own galaxy together, or have Ahsoka and Sabine follow Baylan and try to figure out what he is doing as well as possible 'Secrets' either with the Father, Son, and Daughter, the Witches of Dathomir, or the World between Worlds.
I don't see the need to see what Thrawn is doing or see what is going on with Hera and the New Republic in Ahsoka season 2.