Well, you're right--by making one decision he changed things and has to accept responsibility for the consequences--but that, after all, is what a hero *does.* When he is Superman he is *constantly* going to be taking actions that will have profound consequences, and some of them are going to be negative ones--choosing to save one person may mean another dies. That's a "reckoning" he has to live with. And he was interpreting Jor-El's prediction as punishment, so you're right, he was making a choice--but as Martha pointed out, it wasn't a choice he was literally given between Jonathan and Lana. It was a choice to act when he could, or not to act--I don't think he can be blamed for choosing action, there.