Wouldn't it be possible to reserve map space north of the north pole or south of the south pole for battle maps (and disallow wrapping around there)?
I am not sure how the Civ engine would react to extending the map size while playing (although that might be possible as well) but it should be easy enough to change some map scripts to leave space (as e.g. a special unpassable terrain type).
Then you can carve out some battle maps from that territory whenever you need them, still surrounded by unpassable terrain so the battle participants can't escape.
I'd also suggest to use two phases. One the normal one on the big map, then when that is finished, take all movement points from the normal units so players can't move them and spawn the battle participants on the battle maps (depending on which units initiated a battle in the normal turn on the normal map).
I am not sure how the Civ engine would react to extending the map size while playing (although that might be possible as well) but it should be easy enough to change some map scripts to leave space (as e.g. a special unpassable terrain type).
Then you can carve out some battle maps from that territory whenever you need them, still surrounded by unpassable terrain so the battle participants can't escape.
I'd also suggest to use two phases. One the normal one on the big map, then when that is finished, take all movement points from the normal units so players can't move them and spawn the battle participants on the battle maps (depending on which units initiated a battle in the normal turn on the normal map).