Let me start by expressing how much fun I've had with the new commander battle mode. It's surprising how enjoyable it is to lead a bunch or brain-dead AI around. Setting up volleys, charges, weathering musket fire and opportunistic cavalry. That said with any new form of game play it has its own unique set of problems that need to be addressed. The most obvious of which is the way rounds can by unbalanced in a way that one team doesn't have a chance of winning.
In a traditional multiplayer game the balance of power is held in the hands of the players. Their skill dictates the winner and is just as important as player count. While commander battles have their own skill set, the players have to use the AI to demonstrate their tactical ability. The problem is in a fight between AI, the difference between having just a few more men can be more important than the skill of the players commanding them. In a 10 v 10 fight with 20 men each, the difference of just one player can give a huge competitive to the opposing team. The imbalance only gets greater when the teams get smaller. This means that at the start of a round when one or two people people leave taking with them their AI, the outcome of battle can often already be decided. This problem only gets worse as players get better and the competitive margin gets slimmer.
I propose that in the event of a player disconnecting. Instead of killing all their men or sending them to aimlessly roam edge of the map, they are given to the highest scoring player of a similar troop type, if that player already has an extra squad then it's given to the next best candidate. If no player with the same troop type exists then the soldiers are automatically given an order to charge. I'm not sure how technically feasible it is to exchange soldiers mid-game, but since the Napoleon Wars team is working with Tale Worlds I'm sure that kind of functionality could make it into the next version of Warband.