obstruction

[Mountaineer]

I umpire almost every level of softball from LL, HS, ASA, NAIA & NCAA. I had a play tonight in HS fall ball I had never seen before. Since it was fall ball we work alone so it was all mine to sink or swim with. Here's the play:

R1 on 1st base with 2 outs. Batter hits ball into right/center field. R1 rounds 2nd heading for 3rd and the throw is a rope from the center fielder well before R1 gets to 3rd. She turns back to 2nd and is now caught in a run-down between 2nd and 3rd. In the meantime, the batter-runner has now achieved 2nd base and is proudly standing there. A defender chasing R1 toward 3rd throws the ball to the 3rd baseman and stops in the basepath. R1 now turns back toward 2nd and runs into the fielder and they both fall to the ground in a heap. The 3rd baseman comes and tags R1 out - I've clearly got obstruction. My question is: where do I put the runners??

I've asked several other umpires from the area here already tonight and have gotten several differing opinions. I put R1 on 3rd and actually thought I was wrong in doing so. I thought she should go back to 2nd but didn't know what to do with the batter-runner. I think I know the correct answer now, just wondered what you all think.