Be it from

  1. He ran from the battle; be it from cowardice or fear. He must be disciplined.
  2. Be it from cowardice or fear, He ran from the battle. He must be disciplined.
    If both are literary way of expression, please make them in ordinary way of expression.
    Thanks
  1. He ran from the battle. Be it from cowardice or fear, he must be disciplined.
  2. Be it from cowardice or fear, he ran from the battle. He must be disciplined.

Other punctuation possibilities exist, but definitely not the ones you have used in the original.

Neither are particularly ‘literary’ but in a simplified format they mean:
He ran away from the battle and he must be punished, regardless of whether he ran away because he was scared or because he is a coward.