I've little doubt that if they'd both lived, Thrawn would finally have eliminated C'Baoth. The nut was powerful but too unstable to ultimately succeed even without Thrawn, Mara or Luke. Some competently smart general from either the Republic or the Empire would have eventually offed him.
Thrawn, I think, would eventually become all the more dangerous. A massive blow to his self assurance might have made him all the tougher.