There's one thing you can do to help prevent lock-ups mid-battle:
Disable the cut-scenes (when the enemy general is killed; when a wall comes down or whatever...) which is IIRC part of the preferences text file.

These cut scenes tend to be a bit of a hit on your hardware compared to the rest of the battle.

Post battle CTD's can be alleviated by giving the e~005 app time to do its cleanup work. A good measure would be to wait until the victory/defeat music has finished.