How would you score this and why...
Runners on first and second. Batter hits to shallow gap between CF and LF. Runners hold up thinking it should have been caught. Runner on second gets thrown out at third on the force.
I would score it as a hit. If you score as a fielders choice the batter is not credited with a hit. The OP makes its sound like a hit and not an error. My interpretation of a fielders choice is if the fielder wanted to go to 1st to get an out but attempts on a different runner it is a fielders choice. But if they could not have got the batter and there wasn't an error it must be scored a hit.
Don't penalize the batter.