One thing I recall some people not liking about Jonathan Kent in MoS, was the way he reacted towards Clark's decision to save his classmates who would have otherwise drowned.
"What was I supposed to do, just let them die?"
"Maybe."
I thought it was great script writing, as it depicted just how confused Jonathan was as well on what he felt was best for both parties. A lot of people felt this was not how a classic, traditional Jonathan Kent would have treated such a situation. Suggesting that perhaps Clark should have in fact allowed children, or anyone for that matter, to die. What I do like about the tornado scene, is that Jonathan didn't exclude himself from this. Had he wanted Clark to save him, I do think it would have been a bit selfish on his part to suggest that he perhaps let a school bus full of children perish, but when it comes to his own life, then make an exception and allow Clark to save him. I'm not sure what kind of an example that would have set for a young Clark.
I felt that Jonathan's sacrifice in this scene set the tone for what was to come in the film, and gave Clark/Kal the courage to make his own sarifices by sacrificing himself for the safety of Earth when Zod first shows up, destroying the world engine over the Indian Ocean in what was nearly a suicide mission (the most powerful scene in the movie in my opinion when it showed Superman flying up the powerful beam the world engine was emitting, while Perry took Jenny's hand), destroying the scout ship that would have enabled the re-population of his own race, and then finally, ultimately killing Zod, what he believes is to be the last of his kin.
When Superman sacrifices himself for us, he does it 100%. That's why he's Earth's greatest champion, and even though a fictional character, is still treated like a messianic figure. In this film, I think Jonathan's death helped give him the courage to be able to do that.
I love the line towards the end of the film when he and Martha are visiting Jonathan's grave, and Clark states, "I just wish he was here to see it," and Martha replies, "Oh he saw it Clark, believe me."