When viewing the events of Star Wars through Thrawn’s perspective, the Chiss are downright reasonable. Unlike more one-dimensional villains, like Palpatine (Ian McDiarmid), who is only interested in obtaining power, Thrawn has a much more complex motivation. Hailing from the planet Csilla, the Chiss are xenophobic, believing that they are superior to all other races. This is not to say that Thrawn is on the side of good; his backstory merely makes him a more interesting villain than most.
When Csilla’s sun began to die, Chiss society, known as the Ascendency, turned to the reaches of space, which led them to partner with the Empire. The Empire had the resources for the Chiss to utilize. Uniting with a dictatorship was logical, especially for this society. The Chiss Ascendancy is stronger than the Empire, so the New Republic would not be useful in helping them.
These motivations are not explored in “Ahsoka,” and nor would they be. Thrawn is calculating above all else and not the type of villain to announce his plans. But from the mouth of the character’s creator, Thrawn’s devotion to his culture is the obvious reason for his actions. Anyone would want to save their society, especially if they were raised to believe theirs was the best. After being stuck on a remote planet for years, Thrawn would undoubtedly want to return to the galaxy we know and raise the Chiss to the glory he believes they deserve.