Still the other is trained to kill exactly this kind of targets (nobles, leaders) in 1 on 1 assassinations he doesn't have leadership nor other capabilities - all of his purpose in life is focused on this.
And he should not fight him in a fair duel, but stab him when he is unaware.
Hmm, what brings me to another idea - give the attacked commander 50 fatigue on the start of the battle to represent that.
Maybe with mod #onebattlespell on the assassin with a spell with 100 precision that deals 50 fatigue damage.