Balk Called, is it accurate?

[Coach AJ]

Clarification would be appreciated.

Situation: Runner on second base, batter at the plate.

Issue: Pitcher legally delivers called strike, and receives ball back from catcher, at the front of the mound, but still on the dirt portion. Pitcher turns, starts back to the rubber. Without reaching the rubber, the pitcher throws to the shortstop, who is in his normal straight-away fielding position, and the shortstop then chases the runner, who is leading, back to second base. Umpire calls a balk, saying the pitcher threw to a position player and not to an occupied base.

Our claim is since the pitcher never returned to the rubber, he should be allowed to throw to the shortstop. There is no issue with deceiving the runner, since the pitcher did not return to the rubber to face the batter. Are we right?