Perhaps some mechanic could be given to the player that allows various conditions, when met, auto pauses the battle so those conditions, after being met could be resolved int he following Phases/Turns.
Example:
When Battle Group A encounters enemy Battle Group B, if/when Battle Group A's total manpower strenght drops below 15% AUTO-PAUSE.
If your Channeler gets into a conflict and his "mana" drops below 30%, AUTO-PAUSE. etc etc.
That would/could allow for winning fights to carry forward and losing ones to be paused for re-thought before total destruction of certain units could be suffered.
If a strong mix of possible "conditions", even ones that auto executed other conditions, would allow for great flexibilty and freedom while also providing a stop gap for the infamous BIO break. 