Agreed. If you think having Supes kill Zod was sacrilege, having an alive Jor and Lara be Villains would have been Jason White levels of franchise poisoning.
What I would have liked if maybe Faora or Jax-Ur be the main antagonist of MOS,and save Zod and his army and the Black Zero stuff for an MOS 3 or Even as the main opponents of Justice League.