I had a similar situation...my team batting...one out...runner on 1B...two strikes. I sent the 1B runner at the pitch...swing & miss by the batter...drop by the catcher. Batter runs anyway, as she's been told, and the catcher throws unnecessarily down to 1B.
The ump correctly called the batter out before the throw, but he ruled that my batter running to 1B "confused" the defense, and he put the runner who stole 2B back on 1B.
Wrong, wrong, wrong. The defense is responsible for knowing the situation and making the appropriate play. The advance of your base runner should have stood.