I can see how prisoners could get annoying. What I was thinking was making it some sort of stance for your units. Along with aggressive, passive, you have a take prisoner option, where if you overpower the unit it goes to your prison, it obviously has to be more difficult to take them prisoner then to kill them, and I don't have any ideas for that. Then when there in prison, you have to feed them food (so that you don't want to have to many of them) and to get rid of them you can trade prisoners with other players, maybe use them to increase relations or trade for resources and/or your own troops back. You also could just execute them maybe give experience to the unit that killed.