If your doctor can’t treat your suffering in a satisfactory manner by means that don’t have the contraceptive effect, it is morally OK to treat the symptoms that afflict you with a method that has an unintended contraceptive side-effect. You could resume relations with your husband, too, if your personal circumstances were to allow that again. There wouldn’t be a moral issue with that. Under the conditions you’re describing right now, there wouldn’t be a morally-compelling reason to prefer to avoid the contraceptive effect. If you and your husband got back together into the same household, though, you’d want to see if a non-contraceptive treatment would work satisfactorily.
I hope that makes sense. For instance, women in a convent and other chaste unmarried women don’t need to concern themselves with whether their medical treatments have contraceptive effects. I mean, they couldn’t look at two equal alternatives and think, “Gee, what if?” and choose the contraceptive “just in case”, but if that is not their intention, they don’t need to concern themselves with it at all. Married women whose husbands have become permanently impotent wouldn’t have to concern themselves with it. Married women who need to be available for marital relations can accept treatments with contraceptive effects if no good alternative exists, but they have some responsibility to look for treatments that don’t have those side-effects.