Runner goes on ball three

[emaxos]

Watching Dixie Girls Debs District playoffs (16-18). R1 on third, 2 out. Ball 3 called on batter. Batter takes off for first base as if she thought it was ball 4. She takes big turn past 1B and heads to 2B. Defense overthrows ball to 2b, R1 comes in to score. BR pulls up on 2B.
PU never said anything while things are unfolding.
PU then calls time, consults with BU on the count, then they nullify the run, bring R1 back to 3B and batter back in the box, and continue.
In discussions that follow with fans, I say run should count.
I base that on the discussions I have read here about D3K with 1B occupied, less than 2 outs, and BR runs to 1B and others advance. Consensus here is the defense should know not to make the throw. Is the ball 3 situation different, and if so, why?