[Skahtboi]

Okay...for what it is worth, here is my take on this.

You should have never allowed the pitch to the batter who had three strikes, period. That part should have never happened. You could stand there the rest of the day, if necessary, and kept repeating to the coaches and the batter "that was strike three." Sooner or later, somebody (as has already been stated) would have figured it out. The the batter would have run or returned to her dugout, with the outcomes being the ones the Tom has already stated.

Once you allowed the batter who had struck out to be pitched to, you placed the offensive team in jeopardy of a BOO. Once again, you cannot do this. An umpire cannot place a team in jeopardy of being penalized either by his action or inaction, as in your case. You also put the defensive team in the untenable position of giving up runs they would have otherwise (maybe) not given up. You can't do that either. The only choice you had at that point, IMO, is calling the batter out and returning all runners to the base they occupied at the time of the pitch (2 and 3). You would now have one out. New batter. You will probably receive a bunch of flak, but because your inaction created the mess to begin with, you should happily take it and use it as a learning moment.