Quick Rules Question

[referee99]

USSSA Slow Pitch.

Runner on 1st. No Outs.
Batter hits line drive, caught by the pitcher...
... who throws the ball to 1st in attempt to double up the runner.
Ball sails over 1B's head and out of play.

My partner gives the runner just 1 base, I suggest that it should be two.
He says something about the runner not having gotten back to 1st base when the ball went out of play being a factor....

Proper ruling here?