The "knoick out" scenario is a late addition, and additions like that easily cause some leaps of faith if you introduce them without adapting the main story.
I did the evil route and though we gloriously massacred the false-god believers, Minthara was still imprisoned on return to moonrise towers, and given to the inquisitors for torture. Just because she had failed to find the artefact. The goblins that accompanied her were unceremoniously murdered in the throne room. (Actually it was "us" who murdered the poor goblins, who thought we were their friends and allies, to gain the trust of the MT absolutes)
So yes if she loses the battle, she should know that a gruesome fate awaits her. But where else can she go ? She's still under the influence of the absolute. No way out for her but death.
I think I would also prefer a swift death on the battlefield than become a playtoy for Myrkul fanatics.
