This is baseball, folks!
When continuous play is still going on, you can't just stop it by calling time. Nor does it stop just because the pitcher has the ball on the pitcher's plate. The batter/runner may run to his heart's content until he decides to stop or is put out. If the pitcher and catcher become set, you may have a leaving early violation if he doesn't get back on the bag and stay there. We all know the only penalty for that in LL baseball is the runner is sent back, or, if the ball is hit into play, anything other than the bases EARNED by the batter are taken away.
Design a play to protect against the Batter-runner advancing, or just ignore him to prevent the run. He can only go to second unless the runner on third scores. And, you still have an open base to work with.
Umpires are not going to assist the defense by calling time to prevent runners from advancing, either in this situation or in situations where the ball is being thrown back to the pitcher.
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