Why did Sister Mary Virgil say "we women must learn to control our emotions?"

The quote you mention comes from Chapter 18. In this chapter, Bill Lamb pleads with Sister Virgil not to expel Toycie. Similarly, Miss Eila (Toycie's aunt) begs on bended knee for Sister Virgil's understanding.

However, Sister Virgil is resolute in her decision to expel the young lady. Apparently, the school's strict rules and the potential, negative reactions of other parents are enough to stymie Toycie's future prospects at the institution. Bill argues with the principal, citing Miss Eila's incredible work ethic and the small family's destitute circumstances as credible reasons for leniency. However, the principal is impervious to his entreaties.

In a fit of frustration, Bill proclaims that, since Emilio Villanueva will not be punished for his part in the affair, Sister Virgil has no cause to expel Toycie. After all, Emilio is just as responsible for Toycie's pregnancy as she is. Sister Virgil's answer exhibits her inflexibility and lack of compassion:

In cases like this, we believe it is entirely up to the modesty of the girl to prevent these happenings.

We women must learn to control our emotions...There are times we must stand up and say "enough" whatever our feelings. The rate of illegitimacy is quite high and has been high for a long time. The women will have to decide for a change in their lives, otherwise they will remain vulnerable.

Sister Virgil's words also betray sympathy with the patriarchal conviction that a woman holds the reins of moral sanctity in her hands. From that point of view, it is considered the woman's responsibility to 'rein' in her own sexual desires and to be the gateway for modesty. Since she will be the one most adversely affected (both socially and economically) by an extra-marital sexual union, it is she who will need to choose how far she will succumb to the male insistence for consummation. Although Sister Virgil's words are hardly compassionate, she is convicted that her position is infallible. Thus, her words to Bill Lamb and Miss Eila are intended to convey the message that no further arguments for leniency will be entertained.