[cartman]

I don't think the runner is protected while on base. MLB rules call a runner any offensive player who is advancing toward, or touching, or returning to any base. If the runner gets hit by the ball on the way down (and they are the first player to touch the ball), they are out.

edit: something similar came up in a game the other night. It was a ground ball, not a popup. The player running to second saw that it was likely going to be fielded by the 2nd baseman for a double play, so he held up and let the ball hit him. He was called out, and the batter got to stay on first. It was a novel way of breaking up the double play. But that was also MLB, softball might have a different rule.