i don't think it matters if u kill them during the battle or kill them after. But if in the middle of the battle and ur army is routed, then the prisonors u capture will be free by thier comrades chasing after ur soldiers. but i always wait towards the end, just to see how many prisonors i can catch. and i won't worry about the bad vices, unless ur army is low moraled, or the troops are low moral types.