So, the carefully balanced war is shot to hell. Palpatine isn't going to be able to pull of a PR coupe large enough to overshadow the fact his home system just defected, unless he convinces everyone that the Organization of the CNS itself eats orphans. He needs to push the CNS into the sphere (and control) of one of the other groups if he wants to maintain any semblance of continued control over the situation, and no matter what, I don't see that happening.
Spinning Bacta world as war profiteering might take some heat off him, but at this point, with Naboo, the CNS is a very active referendum against the whole existing mess.
So, violent shenanigans inbound, I suppose.