Birth control pills sterilize the body and sexual energy. Therefore, the roots of the Tree of Knowledge become seriously malnourished, inhibited, and affected.
There are exercises to heal oneself of menstrual irregularities without resorting to chemicals, if that is her will. The book
Esoteric Medicine and Practical Magic has some different treatments you can find by looking up the term “menstruation” in the index. This should be combined with sacred rites for rejuvenation.
However, regarding your partner’s choices:
There is no coercion in religion. —Al-Baqarah 256