It all depends, I guess, on how she viewed those Shadowlings who failed her once: there are many examples ih history where there is more tolerance given for a valiant enemy effort (or that of an allied troop) then for the failings of one's own troops. I suspect that the Main was of much greater significance to her plans than Noctus was, and I am not sure if she'd be willing to cut more slack to a talented human than her very own commander.
There is also the twist about Noctus being revived, but not surviving the Shadow War. Personally I think that she might as well have revived Noctus, but given him a temporary demotion, and that there is a chance he survived the end of the Shadow Wars, such that we might catch a glimpse of him in TSoG.