I sort of don't mind if JK lives or dies. But I feel like him dying fits more with the tone of this film... I have a hard time seeing Clark moping in Alaska with both his parents alive and well and with no motivation to do so...
As for it being too much like Spiderman or even Batman, I just don't think it is.
Spiderman - Uncle Ben dies, teaching Peter that his powers are not just for his own selfish gain, and forcing him to feel the responsibility that comes with such power.
Batman - The Wayne's die, and it fuels Bruce's life with anger and hatred which he focuses into fighting for justice.
MOS - Jonathon dies in a tornado while he is off rescuing other people (who may even not be grateful for his rescue, and view him as a freak), and it forces him to face the harsh reality that no matter what he does, he can't save everyone. It takes the events of the story, and a woman like Lois Lane, to convince him it's what he CAN do that matters.
I think they are very different lessons, all learned through the death of loved ones.