I can't be sure if the hero is a boy or girl because looking at the illustration he could be a tomboy or a trap and I don't know if the Goddess is good or evil, but the reason that she wants to kill him isn't because he's going to turn evil, but it's because of his skill's side-effect.
He basically possess something along the lines of infinite growth, his magic power will keep increasing till the point that a small fluctuation in his emotions can make his MP run amok, causing an explosion that will erase all live in the world. He's literally a time bomb that will destroy the world.