When to call time??

[DaveASA/FED]

R1 on 1st, hit to right field, throws to first BU calls BR safe, throw from F3 to 3rd going after R1, as PU I am down there for the play and call R1 safe. She requests time to get up from slide, I start to call time and see out of the corner of my eye that R2 (BR at start of play) is heading into 2nd so I wait to call time till R2 is on second.

So question is what if I would have called time prior to R2 getting to 2nd? 3rd base was not thinking about throwing on R2 and didn't, was doing the hold tag until runner gets up thing.....but what would you do if you killed it too early? Let R2 continue to 2nd? Send her back to 1st? What say you all??