If I were a betting man I'd say they would have it so that Thrawn's fate is left ambiguous if he does bow out at the end of this season (as is the norm it seems with Rebels).
As [member="Xiarr Sair"] mentioned, I could see Filoni having it mirror Legends with him being sent away to map the Unknown Regions as punishment for not entirely destroying the Rebel Alliance, but is still too much of a valuable asset for the Emperor to have him killed.
For me personally, if there's anyone who knows how important Thrawn is for folks, especially the fact he's now canon, is Dave Filoni. And the guy is pretty much head of Star Wars Animation now so I can see him leaving him alive for potential future use.
I mean there's thirty years between Episode 6 and 7, who's to say there's not another animated show somewhere in there.