There are legitimate reasons to take birth control pills as hormonal treatments for different conditions, but the ethical implications of it are complex, because it depends on the old double effect argument. Double effect is a principle from St. Thomas that says you can do an action for a moral purpose that might have some secondary effect that is harmful and would be immoral in other circumstances. For instance, if a train is going to run off a cliff, it is licit to switch the rail so the train avoids the cliff even though this might cause it to run over a person on the other track. Double effect reasoning is definitely valid, but it can be applied very promiscuously by some theologians, used to justify almost anything. An important principle that has to be born in mind is that of proportionality: there needs to be some significant difference in proportion between the good effect of an act and its bad secondary effects. That makes medical use of birth control a tough subject, because you have to ask, “Are the health needs of a woman of such gravity that she can use a drug that could cause to to abort an embryo?” Usually the answer is no, but there are cases where “yes” is defensible, most obviously for women who are past childbearing, or single and chaste.
The good news is that most (not all) of the conditions you can use birth control to treat have alternative treatments as well, though not all doctors are equally informed about them. Women who have conditions that can be helped by taking birth control shouldn’t go it alone, but should contact their diocese and consult with someone who is well versed in Catholic bioethics before making the decision.
I was prescribed birth control pills for over 5 years (10 different prescriptions) by doctors who thought my gyno problems were hormonal. It turns out they were wrong, but that’s another story. 
