A - Thanks for the question. Pope Paul VI stated in Humane Vitae:
“On the other hand, the Church does not consider at all illicit the use of those therapeutic means necessary to cure bodily diseases, even if a foreseeable impediment to procreation should result there from—provided such impediment is not directly intended for any motive whatsoever." (HV 15).When the purpose is medicinal and not for contraceptive reasons, it can be permissable - in some situations - to use the pill as medicine.
Most doctors know the easiest route to treat a problem and that usually involves some kind of prescription. There are other treatments, but they can be more expensive and you might have to search hard to find them. I highly recommend you call the Pope Paul VI Institute or see a pro-life Ob/Gyn to discuss these issues. I can recommend one to you here in College Station. They might be able to recommend a course of treatment that won't have as many side effects as putting you on the pill.
I am guessing that you are a college student and if that is the case, then I am guessing you are not sexually active - therefore there is nothing wrong (presently) with taking a birth control pill to treat a health issue, but there are other options.
If you are married, then I recommend you seek out alternatives to the pill and only use it as a last option, if necessary. Remember that there isn't always just one way to treat a health issue and different doctors might have different treatments they would recommend. One of the things you would want to avoid is the fact that birth control pills can cause chemical abortions, so other options (many times much better options) that a pro-life doctor can help you with would be what I would highly recommend.
I hope this helps.