Ironically, he'd actually be better off in the historical HRE. Doing nasty things to your own citizens was fairly normal back then, but doing nasty things to the captured enemy wasn't, because that means the enemy would do the same and one day it might be you that is captured. So treatment of the upper classes was very frequently civil. As an Officer it would be taken as a given that that Qrech is also a Gentleman and therefore his solemn oath would be all that was required to give him parole, and then he'd be free to live out his life in a carefully-chosen town in the Empire until the end of hostilities, a formal exchange of prisoners is performed, or a ransom is paid. He might even be released back to the Skaven Empire as long as he swore not to engage in hostilities against the Empire, basically acting as though he was a prisoner but free to return home until the sides meet in a truce and say "okay, this amount of released prisoners on both sides are now once more permitted to serve their country militarily", at which point both Qrech and an equivalent Empire soldier (who had sworn the same oath and had been released by the Skaven) would both return to military service.