Am I right to tell my CCD students they should not take the pill for medical purposes?
You are conflating prudence with a moral requirement. By saying it is not okay, you are giving your students the impression that there is a moral prohibition against taking drugs ordinarily prescribed for contraceptive purposes for other legitimate medical reasons. Your reason for doing so, though—the ineffectiveness of such a treatment—is a prudential concern. There are other prudential concerns (e.g., it could weaken commitment to chastity), but it is unhelpful to blur what should be a sharp distinction between prudence and moral requirement.
Explain forthrightly that some drugs have more than one purpose. They can be taken for a good purpose (e.g., to regulate cycles, to treat acne), and they can be taken for a bad purpose (e.g., contraception). If a drug that has both effects is taken solely for the good purpose, then it is okay to take that drug.
But we should be certain that such drugs are the best possible means of treatment. Since there are reports that the pill only masks symptoms and does not treat the actual malady, it may be better for teens and their parents to explore alternative treatments that will seek to cure the problem. One Catholic apostolate doing work in this area is the Pope Paul VI Institute (www.popepaulvi.com).