Whilst it would be kinder to Emma for the baby to be a boy, and Charming did want a boy, there is so much potential story if the baby turned out to be a girl.
Snow described the relationship she has with Emma as not what she “wanted”. If the baby was a girl, Snow would get the daughter she always wanted.
Emma would feel rejected by Snow, and jealous that her new sibling would be getting the childhood and parents that she should’ve had. Emma would feel that the new girl is replacing her in her parent’s hearts.