Runner collides with on deck batter

[Gmoore]

Runner on 2nd and 1st batter hits a ball into the gap runner on second comes around 3rd and going home on deck batter thinks she needs to get the bat out of the way and goes to pick it up, the runner going home collides with the girl picking up the bat, the ball is thrown to cut off person standing at second.

Is this considered assisting the runner? I was told that I should have called the runner out and returned the runners to the base they occupied at the time of the collision.