NCAA: Runner in contact with base is hit by batted fly ball

[teebob21]

Had a good tricky one today on the dish, something that I've never seen in all my games ever: No outs, R1 on 3B, R2 on 2B. Batter hits a soft shallow low fly ball down the third base foul line. R1 takes two steps to home and retreats to 3B. She is standing with her back to the plate on 3B and the ball hits her in the back over fair territory. No fielder had an opportunity to catch the ball.

I signal fair and drop the signal (far too quickly) and continue watching. The ball rolls in the infield and is picked up by an infielder (F5 I think). R2 is daydreaming and is nearly put out at 2B. The BR has only gone 15 feet down the baseline, and the defense puts her out at 1B.

One out, right? All of a sudden I have the defensive head coach in my ear wanting an out at 3B. I've already looked up the rule, but on the spot, what would you have here?