Tough call for me today

[DTQ_Blue]

I posted this on the softball board because it happened to me in a softball game today. I am curious what the call would be if this happened in a baseball game. I can imagine it happening with young kids.

Tournament game today. Runner on 3rd, 1 out, batter K's but pitch gets by catcher. Runner breaks for home, batter stays in box. Pitcher comes in to cover plate, batter still in box fails to clear the area around the plate as catcher throws to the pitcher. Runner somehow gets thru to the plate, throw from catcher not caught by pitcher and is rolling in infield. Batter still standing in the box.

How would you handle? It happened to me today.