little league majors div rule

Question
Bottom of last inning and home team hits 2 run walk off home run.  The batter crosses home plate before the original baserunner that was on first when home run was hit.  This occured while team was celebrating and mobbing batter and runner down third base line.  Visitor manager tells umpire that should be automatic out.  Umpire says "do what you have to do".  There is no ball anywhere due to home run.  Umpire then gets ball from home manager and rolls it onto field in front of home plate.  Defensive infielder then takes ball and steps on home then proceeds toward home dugout where team is celebrating and tags both runner and batter.  Umpire calls "safe" and then "ballgame".    Shouldn't the batter be called automatically out after crossing the plate prior to baserunner?  Does that play require the pitcher to go to the mound after picking up the ball the umpire rolled out to step off rubber for an appeal?

Answer
Hey Steve,

It seems to me that the runner should be called out. This is why you run the bases after hitting a home run. On the other hand people could argue that this is why it is called an "automatic" home run.
I would have protested the call.

I'm not too sure on this one.

Dennis