The problem is I think people are presupposing that Jonathan has some concept of what a "superhero" is, and that Clark was just always destined to become that.
I'm not presupposing anything of the sort. You don't have to be a superhero to help people. In other versions, Clark didn't learn to be Superman because his parents groomed him to be a superhero; he learned by watching their example as kind parents and good neighbors, people who always helped out other people who needed it, people who were unselfish and generous -- and people who had faith in the goodness of the people around them and thus inspired the best in them.
That's what this Jonathan lacked: faith in humanity's basic goodness. He was a fearful, paranoid figure who taught his son that humans were just as fearful and paranoid, that they'd never accept him because he was different and so he should perpetually hide himself. And one of the few things the movie got right is that Jonathan was absolutely wrong. Superman did meet with some initial suspicion, but he quickly proved that he was here to help and that he was a force for good (as long as you disregard the ill-conceived, badly-directed action sequences where he totally ignored all the lives being endangered by his superfights in the heart of populated areas). So instead of the usual story where he becomes Superman by embracing what Jonathan taught him about basic human goodness, in this version he becomes Superman by acting on his own basic instinct to help and renouncing everything Jonathan ever taught him about what a bunch of xenophobic, tribalistic creeps humans were. This is a movie about Superman proving Jonathan Kent wrong. The tragedy is that it took him so long to finally step up and defy the bad advice his father kept giving him.