[Saulot]

Ignoring for a moment that this is a pretty big change, your idea has merit. However, late game, when you have tons of mages and commanders, it becomes difficult enough to keep track of who dies where as it is, with spell attacks. Silent Assassinations with only a message that somebody named 'Ensign Ricky' died makes it far too complicated and unpleasant.

Besides, even if your commander dies, somebody should spot the assassin assuming the commander wasn't completely alone,... I mean if it's a giant earth elemental, you couldn't miss that, an ashen angel descending from the sky and flying away afterwards, an abysian slayer with charred footprints left all over the place, etc.