At least some of the news reports indicated that the aircraft "flew through" a thunderstorm, but looking at at the Flightaware track of this flight, it appears they did not fly through any cells. They diverted along the south side of a line of level 6 storms extending from northeastern Colorado into Kansas and Nebraska.
Not far enough south evidently. Intense hail is a real possibility beneath the anvils of supercell thunderstorms - even many miles from the main core of the cells.