This is a case where it's easy to see the outcome, but impossible to see the motivation. Lightning is one thing that really scares me on a ballfield (fastballs, breaking balls, knuckleballs, ground balls and fly balls do, too
)
I will never fault an umpire in a baseball game for stopping play at any time when he feels lightning is that threatening. Even in the middle of a play, and especially at the lower levels. If such an action leads to a protest, so be it. At least all the principals will be able to testify, and the umpire will be able to look himself in the mirror.