the clone wars and the prequels have already invalidated the Thrawn Trilogy. Look at all the contradictions in it now.
You mean besides the account of the Clone Wars that was kept as an S-Canon rumor due to the fact that anyone witnessing the actual attack by clone troopers on the Jedi, without knowing of Order 66 would see them as insane? That was pretty much it. The actual storyline in The Thrawn Trilogy is still considered C-Canon.