the clone wars and the prequels have already invalidated the Thrawn Trilogy. Look at all the contradictions in it now.
Again, the only reason why the Thrawn trilogy has all the contradictions it does is because it was written before
any of the events of the Clone Wars were made canon. At that point, Zahn was guessing what was happening, and even in the 10th anniversary of Heir to the Empire, Zahn says that Lucas made him change a lot in that book, and in the trilogy, to better fit the movies. And it's still a contradiction, because Lucas changed his mind on a couple of points (Or didn't tell the author what was really going to happen).
So really, it's still Canon, it just got some facts wrong.