The narrator/daughter in "Boys and Girls" begins to realize that there are expectations of how boys and girls, later men and women, are supposed to behave. In other words, she is at that transition age when gender roles (with their stereotypes and outdated traditional norms) are encouraged by adult figures. Her grandmother indicates these ideas during her visit, saying things like "Girls don't slam doors like that," and "Girls keep their knees together when they sit down."
The narrator is afraid that she will be forced to stop working with her father and made to work in the kitchen with her mother. She would have to start acting like a lady, whether she wanted to or not:
A girl was not, as I had supposed, simply what I was; it was what I had to become.
She resists this and thus expresses what could be considered a feminist critique of traditional gender roles. She challenges traditional notions of how men and women "should" behave.
When she leaves the gate open for Flora to escape, she has no justification for doing so. But, considering her resistance to becoming a girl, this seems like an act of rebellion. She lets the mare (the female) go free; just as she wants to be free to act however she wants, regardless of how a girl is "supposed" to act. Flora is a parallel to the narrator. Both are females wanting to be free.
When Laird tells their father what she's done, he concludes, "She's only a girl," she doesn't "protest" it. She acknowledges that she's a girl, but given her prior behavior, she is hurt that her father would dismiss her in this way. Her act of rebellion is cast aside by saying "She's only a girl." This hurts her more than the guilt of disobeying her father.