"She had known Father O'Malley since ages, when she had become a ward of the Catholic orphanage that he directed"
This could have been written with more intimate feeling, less her and she, that and it´s.
"Knowing Father O´Malley for many years, Mary had become a ward of the Catholic orphanage he directed."
here... "but when she shifted her weight," you could have wrote, "shifting her weight," creating less read and more information
turn your emails on btw, i want to send you a private message, for your benefit