Ruling and OBR/FED cites please

[LakeErieUmp]

This came up AGAIN in an U14 travel game today. R2 takes a HUGE lead off second. Pitcher throws to shortstop who promptly tags R2 out. Coach screams that pitcher can only throw to "occupied base". BU concurs and calls balk.
I've scoured the FED rules (the league plays a mutt FED and OBR rules deal - go figure) and can't find support for a balk on this.
PLEASE when you reply (if you do) point me to OBR or FED rules to support a balk. Otherwise, R2 can take a lead halfway to third and - if this BU is correct, pitcher has to throw to SECOND BASE before making a play on the runner, leading to the inevitable result R2 will make it to third.
Thanks again for all your help and insight. I hope I explained it clearly enough.