I will assume the ball had not passed a fielder when the runner was hit. If so, the ball is dead immediately, the runner who was hit by the ball is out, all other runners return to the last base touched at the time the runner was hit and the batter/runner is awarded 1st base.
If the ball had already passed a fielder and no other fielders had an opportunity to make an out, the ball is live and in play.
The ump ruled runner out, batter safe, all others advanced and the score counted.
Umps may not be right all the time but they are never wrong.....just ask them.lol