I’m not sure I see what the problem is. When the ump agreed to ref the game, he knows that he can be beamed by the ball. That’s the chance he takes.
He didn't agree to be a target. Being accidentally hit is one thing but being intentionally thrown at is another matter all together.
I had to spend two days in the hospital after being hit in the head by a baseball. It is plausible that the umpire is suffering medical issues as a result of being hit. In big league games when a batter is hit cleanly in the head by a fastball, the player is always taken out of the game and put under medical observation as a precaution. Why? Because a baseball can be lethal.