Out for removal of helmet after home run

[clodder]

I am a parent and player, but not an umpire.

Girls 10 y old fastball tournament following CSA (Canadian) rules which I believe are essentially the same as ASA. Two out, two on, and batter hits a home run. Rest of team comes to congratulate her at home plate and she removes her helmet just before she enters the bench area. Umpire calls her out for removing her helmet on field of play, and also says "no runs' because she is the third out.

First, calling an out seems overly picky even if in the rules - is it?. Second, even if the out call were technically correct, was not allowing the two runs that crossed the plate before her correct?