Batter Hit by Catcher's Throw

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This now has happened twice in the last 4 days: FED ball - With a runner stealing 3rd base the catcher attempts to throw them out.

Saturday, the throw hit the bat of the batter who was still standing in the batter's box and then bounced into the dug-out. Last night the catcher let the ball squirt behind them, and the throw hit the batter in the helmet - who immediately went down (the batter had vacated the batter's box in an attempt to get out of the way of any play) and the ball ended up near the back-stop. We judged that neither batter interfered intentionally.

In both situations we left the ball live (dead when it entered the dugout) and the runners were allowed to advance their one base (to 3rd). Is this the correct call? Or should the ball be declared dead at the time of the throw and the runners returned? Should the runner in the first situation be awarded home?

I know this sounds freaky, but it really happened!