I just read an article where the screenwriter explained the 2 pivotal scenes in Man of Steel.
So I am good with why Clark decided within a split second to agree with his dad to not save him.
On Jonathan Kent’s death scene, Goyer explained, “(Jonathan’s) point was not that Clark should never reveal himself, that it was such a monumental decision that he has to be mature enough to think about the implications of what’s going to happen when he does do it.” Goyer continued, “I understand that...some people didn’t like it, and they say, ‘Oh, Superman could have figured it out.’ But what people have to remember is that Clark was only meant to be about 17 at the time.” Saying that Clark was “untested” and “didn’t understand the extent of his powers,” Goyer added, “I don’t believe that Clark could have saved Jonathan without revealing himself…that was Jonathan’s point: ‘You’re not old enough, you’re not mature enough to take this on, because it’s going to change the world.’”
As for the killing of Zod, Goyer explained that the filmmakers wanted to put the young Superman in as difficult a situation as possible, saying, “Again, this is an immature Superman. This is the first time he’s ever flown, just days before that. He’s not aware of the extent of his powers. And he’s fighting somebody who won’t stop — (Zod has) said, ‘You can’t put me in a prison, I won’t ever stop.’” Goyer maintains that the act of killing Zod is what actually leads Superman to vow he’ll never kill again..."
