I don't know much about the chiss but if I remember correctly, I think a Codex entry states they pretty much go hand in hand with the empire since they were conquered by them, could be wrong of course as i'm going from memory here.
You are quite incorrect, it's actually the opposite. The Chiss are the only society that became official allies on equal terms from a civil meeting between leaders. Nobody was conquered. Chiss history lesson time!
The funny thing about all this is in the books previously written about the Chiss, they didn't even become known to anyone outside the Unknown Regions until the Clone Wars era. There was some discussion about this before but to have SWTOR fit in with the rest of the EU you have to believe that at the point where the current Empire fell apart, the Chiss would have disappeared into the Unknown Regions again and all knowledge of each other would have been wiped out and/or forgotten.
People think of the Chiss as being Imperials because of Grand Admiral Thrawn, but he was a bit of a rebel to his own kind, the Chiss never sided with either the Empire or Republic during that time.