Pretty sure that, even when he send C'Baoth off, he's not trying to have him killed. He's trying to put him into a box where he can be stored safely until he might be needed again. For all the problems he causes, C'Baoth represents an irreplaceable resource. Thrawn doesn't have any other dark force users available and doesn't really have any prospect of getting additional ones. He's utterly loathe to waste the one he has, just as he's utterly loathe to discard the Noghri even when signs point to it being a good idea. Thrawn is very careful with resources that have strategic value - very much unlike the Emperor and the Empire in general that was profligate with them. And when his backstory is later revealed it becomes clear why this is the case.

It's worth remembering that, for all the 'we are so screwed' vibes that are floating around Coruscant during The Last Command, Thrawn has, at best, restored the Empire's position to near parity with the New Republic. He has resources and momentum to fight, but the Empire is still at an overall strategic disadvantage and victory is years away at best.