Me and my wife are married in the Catholic Church and we have a baby on the way. She has PCOS (PolyCystic Ovary Syndrome) which brings by itself a lot of symptoms, including infertility. My wife has most of them. The doctor recommends taking birth control pills to cure/reduce the cysts sizes after the baby's birth. We've researched what the Church teaches and we found out that it is OK for her to take the birth control pill, while maintaining sexually inactive.
15. The Church, on the contrary, does not at all consider illicit the use of those therapeutic means truly necessary to cure diseases of the organism, even if an impediment to procreation, which may be foreseen, should result therefore, provided such impediment is not, for whatever motive, directly willed.
What should we do?
Do I have to abstain from sex the whole time she's taking the pill, until the next pregnancy, which we're planning to happen from 2 to 4 years from now?
What do you recommend seeing my wife has PCOS (PolyCystic Ovary Syndrome)? }
Taking estrogen/progesterone pills as medication in order to heal a pathology is not contraception; even though those same pills can be used as a contraceptive. Using some pills for the reasons you suggest can be justified by the principle of double-effect.
When Humanae Vitae was written, however, it was not common knowledge that the common birth control pill, as well as other similar pills, could actually abort conceived babies when the hormonal mechanism for contraception fails. Because of this discovery, that birth control pills can also act as abortifacients, most good theologians would rightly conclude that using the birth control pill even as medication for this reason it is morally impermissible for those that are sexually active. The potential killing of human embryos is not proportionate to the potential healing of the pathology.
That said, there are other medications that heal such pathologies without the moral problems attached. Your best bet is to contact The Pope Paul VI Institute, an organization that specializes in this, and explain to them your problem. You can trust that hey will give you a good and moral solution: