Just for clarification, I love MoS and think Goyer is right that no writer should restrict himself with rules like that. The zod kill was the best scene of the movie, it was so shocking and heartbreaking, but in a good and ballsy way.
Ironically Goyer himself limited the Superman movie by removing all the other choices to stop Zod. No kryptonite, no red sun, no magic, not even that atmosphere thing that made Superman weak. No Green Lanterns with sciencells etc. etc. etc. Anything to illustrate Superman has a brain with which to conduct plans.
Had (some of) these choices been on the table and Superman would have still chosen to kill Zod (to stop him permanently)...that would have been ballsy. And it would have still been the same ending as millions of other action movies.
Leaving the villain alive in an action blockbuster is actually more original and more faithful to the source material.