My mother sighed and vigorously rubbed the head of her son, who was already in his first year of high school.
Literal
Mother [topic-は] sigh [object-を] while-exhaling, high-school first-year [to-にも] became son [possessive-の] head [object-を] roughly rubbed.
がしがし is a rough-textured mimetic — here for vigorous head-rubbing, the kind of affectionate roughhousing a parent does. ため息をつきながら ('while sighing') sets the emotional backdrop. 高校一年生にもなった ('who has even become a first-year high schooler') uses にも for emphasis — 'a boy who is already in high school' (and yet still needs this). The scene captures a tender family moment with exasperated love.