"PU becomes confused..."
Sounds like maybe his "confusion" began long before this point in the game.
If the batter is not positioned properly within the batter's box, the umpire should: a) Call time (if the ball is live); b) Direct the player to take the proper position, and; c) Not allow the pitcher to throw a pitch until the batter complies.
In short, if the batter isn't in the box a pitch should never be allowed in the first place. The chance of the batter being hurt for standing on the plate should be zero.
So what if the player listens to her brilliant strategist of a coach and refuses to follow the umpire's directive to get in the box?
If the player refuses to properly position herself within ten seconds, an automatic penalty strike is called. No pitch is required to be thrown.
I suppose this could drag out for thirty seconds, with a third penalty strike eventually being called. The end result would be the same- an out- but that isn't really the "time killer" the coach is looking for and could possibly take long enough to play out that the game clock would expire.
And it could get even uglier. The umpire has the power to eject a player or coach who willfully disobeys his directives. That might be a last resort, but is a possible outcome. By the time all that is sorted out it's likely the clock will be expired!