The rule should be amended such that in the circumstance where there is a runner on first base the umpire should be allowed to grant him an extra base (over and above the two for a grd, ie. a run scored) if the player on the defense touched the ball prior to it leaving the field of play. Or better yet an automatic run scored which will eliminate the discretion of the umpire.
Note that if this happened with the bases loaded three runs would score, which would likely happen on a regular double in a game situation. This seems equitable to me.