I usually try to make my initial federation with the Thoraxians to avoid this, they're hard to win over.
I will take that advice in my next run!
Laud them enough and make trade routes and you can get them in. You could also make their influence with the Skylaxians high enough to use their special ability and cheat them in.
I feel lauding makes this game much easier. I don't remember this in some earlier patches...
Anyway, Skylaxians have some buildings that gradually antagonize Thoraxian, and my Andors have no Fenerationist party in the government at all.
Currently Burlusts and Evucs are sieging the Thoraxian homeworld, but either they are not really bombing the surface or they are ineffective, as I don't see any significant drop in RCI (yet). Unfortunately, Peltian didn't want to go to war, because they like Thoraxian too much... I might try doing something about that...
but all those wars, I will probably have to put them at halt, before Thoraxian would want to ally with those who were attacking them the moment ago....