I can see that we're definitely focusing on different messages in Jonathan's story, which is interesting and speaks to why I think the story was one of the few really effective Superman moments in the film. One side of it is that Jonathan is telling a story where he had to choose (even if he wasn't aware he was making the choice) between saving his farm at the cost of another, or sacrificing his farm for the sake of someone else's. Superman's actions at the end of the film are certainly his answer to this part of the story, sacrificing his life with Lois for the sake of the world.
However, the side of the story that I focused on was the challenge of understanding the right thing to do in the context of the larger world, and the consequences of one's actions within it. That's the conflict that spoke to me most in the film so it makes sense that it's what I would focus on in Ghost Dad's story. That's the facet of this conflict that "punch the big grey monster to save the world" was not equipped to articulate.
I think that's my biggest problem with the film (well, maybe second to Murderman). I like the themes of the film and the questions it's trying to address. I'm just not satisfied with the way it handles those themes, and I think it falls short of saying something meaningful about them.