Wow. Sorry dude.
In this case, given all you wrote, yes. You did the right thing. You had a lot of quick thinking and teaching to do. There's thinking of the spirit of the game and age you're working with. Taking a hit away from a 6 year old?
BUT... maybe what I would've done is after quietly conferencing with the PU and explaining what the rule was, allow him to overrule his own call (tell him how) and "save face" a little. Then I'd assist with the explanation to the coaches. Then definitely after the game, tell your partner to sit down with a rule book, and NEVER do something like that again.
I see it happen a lot with newbies, especially on fouls. The ball starts foul and they call it right away instead of waiting for it to stop or go clearly foul. He won't do it again.
I'm sure some of my blue brothers will say that once it's called foul it's foul. (But how many HRs around the fair pole have been reversed?) In this case though? Right thing. That's why you were out there with him.