My fiancé has arthritis and is on two medications that halt the progress of the disease and enable her to function at a very high level. Without these medications, the disease would progress and she would experience acute pain. These medications also have the effect of terminating pregnancy. If my fiancé were to become pregnant while on these medications, barring a miracle, she would miscarry. Is the risk of a BCP-induced abortion greater than the risk of pregnancy using barrier methods? Both BCPs and the medication she is on hold the possibility of an abortion. We are praying for the possibility of going off the arthritis medication at some point (pregnancy often brings women with arthritis into remission).
As a prolife physician who shares Randy Alcorn and your concerns about "birth control" pills. Some of my thoughts...
As you well know, you and your fiancé have a very difficult problem with challenging choices. You are right that some individuals do have improvement in arthritis with pregnancy. It is certainly possible that your fiancé could be in this group. I would certainly consider being off the medications while trying to conceive and (hopefully) carry the pregnancy.
As many as 1/3 of pregnancies may end in miscarriage. If a miscarriage occurs, it is possible that the arthritis medicine would not have been the cause of a miscarriage even if your wife were to conceive and miscarry on this medication.
Now for the difficult moral reasoning. Taking a medication for a legitimate and serious medical problem is certainly reasonable for both men and women. Nevertheless, we are certainly called to take all reasonable care to preserve and protect against harm to human life. Thus, I would encourage you and your fiancé to consider learning as much as possible about the signs and symptoms that millions of couples use to practice Natural Family Planning (NFP). This would allow you to identify the fertile times in your wife's cycle so that you can avoid the arthritis medication at those times if you are having sexual intercourse during the 5 or 6 days each month when intercourse might result in a conception. You may already be aware of resources for this technology (such as the Couple-to-Couple league or the Pope Paul VI Institute in Creighton Nebraska).
The academic question of which is the greater risk (BCPs or drugs such as Methotrexate) to the conception is complex; [I] will have a markedly different answer depending on drugs, doses, timing.
In addition, the morality of taking BCP which have no therapeutic help to your wife but clear risk to the fetus may be morally more of a problem than taking anti-arthritic medication that is helping your wife and has an inadvertent (and unintended) effect of harm to the fetus. Rather than delve into this further, I encourage you to consider the options I have noted above. One list of NFP only physicians can be found at this web site: http://www.omsoul.com/.