I think he'd throw in with the New Republic in the new canon. The Chiss in the new canon want an ally. It was the Republic, then when it fell Thrawn hoped the Empire, without Palpatine, could be that ally. A year after ROTJ the Empire runs to the Unknown Regions and exists as nothing but a miniscule remnant of a military force. Its not a viable government ally for the Chiss, and building the Imperial military back up in the Unknown Regions and retaking control of galaxy from the New Republic would be a costly unnecessary venture when the Chiss could simply align with the New Republic.