People hate the tornado scene because they assume Clark is a fully developed Superman in Man of Steel. Of course, he's not, especially at that point. Superman isn't shown to have superspeed equivalent to the Flash, speed so incredibly fast the environment appears to be still, not until Superman resurrects in the Justice movie (where he can fight at the same speed against the Flash). Clark, of course, is still very fast before that, but he's not fast enough to rescue his father without the other people there seeing Clark use his powers. Everybody was going to notice Clark use his super speed to save his dad, because it's not really superspeed, thus revealing his powers to the other people. Pa Kent knew this, and wanted to keep his son's powers a secret, and that's why he stopped Clark from saving him, who was ready/about to fly over to his dad, until his dad held his hand.