Fly 320's, I may be wrong, and the article was thin but here's what I got:
This was a regional (i.e. feeder to the state level) team competition. Her school has no girls team. (that's explicit in the article)
The Worcester Telegram explains her high school has no girls' team, so MIAA rules let her play on the fall boys' team, but only as a member of the team, not as an individual.
Her team didn't make it, despite her help, so they're out and cant go to the next level. This tournament ALSO had individual competitors going to the next level, but she can't be one of those since her exemption only allowed being part of a team. So she can't win as an individual or advance as an individual because her exemption doesn't cover that. Had her team not sucked, they all could have advanced.
There is a Girl's individual competition/season in the spring, and she can compete in that no problem. One assumes the spring set-up will be the same with team and individual parts for the girls, and she'll still have no team*, but can compete as an individual.
Honestly it seems pretty fair. Apparently high school golfers each have a chance to compete in two events. team and individual. since she had no team they let her on her school's Boy's team and kept her in the Girl's individual. That makes sure she also get's the two event model. Would be a non-event, except that she beat the boy's winner.**
* I wonder if the her team can get a mirror exemption and compete in the girl's team event in the spring? Her and her teammates might get another shot.
** If she's that good, she's probably pro level, and will be on tour soon making way more than all of us, and the event directors making the rules. She'll be fine.