So at the end, Clark could not kill Nor.
Not once he realized what he'd done, no. But you specifically said "the instinct to kill wasn't there" and I think what occurred here happened very much instinctively. That's even what Clark describes it as: "Kryptonian instincts like that."
So I think that scene proves that he will kill if he's upset enough and forgets what he's doing. There wasn't even an immediate threat to anyone in that scene, save himself. So it can't even be claimed that he was protecting someone in that instant.
Obviously, this is a difficult issue, but I do think that L&C took a different approach to the idea of Superman killing. He did repeatedly cause the death of others and he did not feel/show remorse afterwards.
I wish we had seen him angst over what happened in BE, but we didn't. The show clearly established for me that our Clark, maybe because he's more human than in previous incarnations, is capable of rage that will overcome him so quickly that he will take someone's life. In that instant, he will not be aware of what he's doing, but he will do it. And he will not necessarily be torn up about it later on, as we also saw on the show.
Just my interpretation of the character, of course, but I think it's a logical assumption to make, given the show's canon.
