Automatic Strike?

[BSBAL18]

Hoping i made the right call, was end of game so i high-tailed it outta there..

Bottom of last inning of championship game, home team down by 1.

2-2 count on Batter, 2 out, runner on 3rd.

F1 comes to set position, R3 takes off home, F1 steps TOWARDS HOME and delivers the ball, while the ball is en route, the batter bails out of the batters box because of the incoming runner.

I called strike 3 on batter because he was out of batters box on a legal pitch ( my judgement was the pitcher delivered a pitch even tho he CLEARLY was throwing home for a pickoff, but his feet and step position was that of a pitch). Mind you, 9u baseball. :-)

Since the batter was out of batters box, the pitch is automatic strike, regardless of where the pitch ends up, 3 outs, game over. R3 was *not* struck by the ball, as i do believe that can come into play as well.

Correct call?