LorienLlewellyn
Make sure she knows how to use her birth control. Make sure she can get to the ob-gyn for more birth control, for paps, for STD tests, and more. Make sure they have a backup plan in case of accidental pregnancy. Make sure they know about STDs and how to protect themselves. Remind her that if they're not ready for that stuff, they are not ready for sex.
Pretty much this. And if she has any questions, take her to see her doctor and the doctor can tell her anything she needs to know.
As Lorien said, if she and her boyfriend aren't ready to handle/aren't equipped to handle these things, then they shouldn't be having sex, but it may happen anyways. Also, I don't know where you live, but maybe there's a legality surrounding age of consent/statutory rape laws? I hate to suggest threatening them with it, but if such a law exists where you are, it might be worth reminding them of it just in case.
Do his parents know they're thinking about having sex? Maybe a call to his parents might be in order?
I realize if they're going to have sex then they'll probably find a way to do it, but I hate to sound like we're encouraging 12 year olds to be sexually active. What if something happened and she got pregnant? If she decided to keep the baby, then some of that decision will fall back on you (as her guardian) and her boyfriend's family.
In the end, if all else fails, as Lorien said it's important for them to be safe and protected if they are serious about having sex together. I don't want to sound too heavy-handed, because I think it's really great that she came to you to ask for help, so take this post with a grain of salt I guess.