Yes, that was ruled a "hit." Konerko was two steps shy of the bag, Alcides Escobar's throw was off line and Eric Hosmer failed to dig the ball out of the dirt. I have no idea how that's not an error on either Escobar or Hosmer, but it was ruled a hit by the official scorer. And the Royals were playing at home, too.
Guthrie would exit the game after 7 2/3 innings and three hits allowed, so this won't be made into as big a deal had he completed the game with a one-hitter. Still, we don't know the action that followed this play would have been the same as it happened with the botched scoring decision -- or if the throw to first resulted in a clean out. The entire mindset of every player on both teams changes once the no-no is broken up.