People fail to realize even 13 years later that there was virtually no other way for Clark to defeat Zod. The longer the fight goes on the more Zod adapts to his new abilities. Not to mention to mention he’s a career soldier while Clark is a rookie. There was no other way to subdue a kryptonian at this time. Especially one who was hellbent on killing every human being. Clark begs him to stop but Zod would have never stopped. So he made a choice that clearly affected him mentally and emotionally. But he did to make sure no more innocent lives were taken.