Why do my berserk commanders disappear after winning fights

[Graeme Dice]

The word your looking for is not realism, but verisimilitude. The rules of the game should obey their own internal self-consistency. A time-limit that arbitrarily kills units that would otherwise be invulnerable isn't particularly consistent. It is definitely necessary to have some point where battles end though, as otherwise it's possible that some combinations could run indefinitely. Two feebleminded sacred statues staring each other down for example.