One is not using “birth control” to treat a disease because “birth control” does not treat disease. Should a person have a disease whose treatment includes hormones that suppress or prevent conception there is no need to abstain.
The good of treatment of disease and prolonging health is a superior good over the known or suspected side effect of suppressing conception. The intent is to treat disease, not distort the martial act, so there is no sin and therefore, there should be no guilt.
The proviso is that the condition be properly diagnosed and that there is no joy taken in the side effect of contraception, which if can be avoided, should be avoided (like any undesirable side effect).