But why does he have to lose that person at all? Superman isn't about tragedy, he's about optimism. He's about family. He's not a grim, embittered loner like Batman, he's someone who, despite his origins as an outsider, feels like he's a full member of his family, his community, his nation, his adoptive species and planet. It's that sense of belonging that makes him so motivated a protector. He lost the world and family he was born to, and he cherishes his new world and family too much to risk letting anything happen to them. It's about the contrast between death (Krypton/House of El) and life (Earth/Kent family), not just death and death.
No, Superman's not about tragedy, but it's still a moment that forces him to grow up and take charge of his destiny in a much more dramatic way, I think.
With the other version, it feels like Clark's attitude is just "Well, guess it's time to head off to the city now, and become a superhero, or something." And then he comes back home for advice like he's just some 20 year old trying to make it on his own for the first time.
It's all just a little too cute and perfect and ideal for my taste, and makes him seem too much like a perpetual kid (never more so than on L&C). Somehow with the loss of Jonathan it feels like he becomes the mature adult we expect him to be in a much more real way.