You don't understand why a blanket statement saying that one sex is inferior to another sex in something is sexist? Please keep in mind that this isn't about pro-level athletes where everyone is in some narrow skill-range. This is about kids. There is a huge amount of variation in skill at this level. In high school sports, you will often have people on the girls team who are better than people on the boys team and vice versa.
Furthermore, punishing someone for their skill and blaming it on his sex is absurd. He's 13 years old, 4'8", 82 pounds. If it's true that he's dominating, then the girls on the high school varsity team just suck. Even if they DO suck that badly, it's no different than when any team has a star player that makes the opponents, and the rest of the team, feel like shit.
It's a clear Title IX violation to kick him off of the team because of his sex.
If they don't want to get sued into oblivion, they'll have to let him play or start a men's team. Starting a men's team means cutting the funding for the women's team in half, cutting their access to the field for games and practice in half, and trying to drum up enough boys to join the team. And then they won't have anyone to play against.