Runner Hit By Batted Ball

[DFM7]

OBR rules. Runner on first being held by the first baseman. BR hits a ground ball that hits R1. My partner (BU), a first year umpire, allows the the ball to remain live stating that because the runner was behind the first baseman and the second baseman would have had no play. The offensive coach was relatively calm but said he had never seen this called in 35 years of coaching. After the game I told my partner that I thought that he was technically correct but I would not make this call unless the infield was in. Any thoughts?