This is a problematic scene for me as well for a couple of different reasons, but I kind of understand Pa Kent's reasoning.
In the flashback sequences to Clark's childhood, we see that the Kents are overprotective of him; this was mostly born out of a fear that people would learn of his unearthly abilities were he to unknowingly exhibit them in public. I think Jonathan feared that Clark would forgo what he was taught [remember the lecture following the bus scene] and fall back on his natural instincts to save others were he in a situation where multiple lives were at stake.
I suppose you could also look at Pa Kent's behavior as a form of parental paranoia. Indeed, it wasn't the tornado that he was afraid of, it was his son's inclination to do what comes naturally to him: saving lives w/ his powers. By sending Clark back to the overpass, Pa was simply trying to reinforce control over him.
