1 foot in foul territory

[ChrisSportsFan]

Ok guys, I'm a basketball official who enjoys occasionally checking in on you guys to help me learn rules as I'm coaching an 11 year old baseball team. We do have some league rules that apply but mostly go with HS rules.

Here's my question: last night, our 3rd baseman was straddling the bag while holding the runner. His right foot was in foul territory when the pitcher pitched. The plate ump called time while the pitch was on the way and said it was a dead ball and called a balk and scored the runner from 3rd. I know everyone (except the catcher) must be in fair territory when the ball is pitched, but did this ump make the right call. I couldn't say anything because I don't know the penalty for violating the rule.

I hope I've explained clearly. Please advise.