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Clark choice is humanity v krypton (adoption v natural). Trying to mix in a choice of Jor-Els Krypton v Zod's Krypton would ultimately confuse the story. So the structure and story must remain as is with Jor-Els conscience providing Clark his first knowledge of Krypton (and being rewarded with the gift of flight) verses Zod as first contact.
Note after Zod's arrival Clark immediately goes to see a Priest, not Jor-El emphasising that Clark is choosing Jon Kent's love (the best of humanity to him) over a heritage he doesn't feel any attachment to.