I am going to have to disagree with the premise of this video entirely. Killing Zod was exactly what this Superman would have done, and it makes total sense for the Superman movies to come. Consider that this Clark Kent was raised by middle American farmers in the 80s and 90s. This was a Jonathan Kent who said "Maybe" when the choice came between revealing Clark and saving a school bus full of kids. This would not have been a man giving his son an iron clad moral code of "Do Not Kill," but more likely a second amendment advocate who believed firmly in "Stand Your Ground" laws, i.e. if someone attacks you on your property, you have the right to respond with deadly force. Superman did just that; he chose Earth as his home, and defended it with lethal force. In so doing, he killed the first member of his own species he ever really knew. This is why he is anguished after the killing; not because he killed, but because he killed the only other Kryptonian left on the planet, making him truly alone just after finding out who he was in the first place.
As for the question of why not kill everyone going forward, this makes perfect sense as well. Superman didn't have a defined moral code going in to this origin story, but imagine a line like this in the next MoS: "The one time I used my power to end a life, it cost me too much, left me too alone in this universe. I'll never do it again." IMHO, that's a much better reason for a person not to kill than some vague "It's a line I won't cross" nonsense. Superman did kill, and he hated what it did to him, so never again.
As for the question of why not kill everyone going forward, this makes perfect sense as well. Superman didn't have a defined moral code going in to this origin story, but imagine a line like this in the next MoS: "The one time I used my power to end a life, it cost me too much, left me too alone in this universe. I'll never do it again." IMHO, that's a much better reason for a person not to kill than some vague "It's a line I won't cross" nonsense. Superman did kill, and he hated what it did to him, so never again.