Dan, I think it's in good hands with you helping to deal with it. It makes sense that you might not want to involve "their" pastor. But it might be helpful for you to consult and possibly involve a pastor they would have some agreement with, even in the narrow doctrinal positions you outline.... with kids that age you want any buy-in you can get from them, at least at the start of trying to help them see things in a fresh light.
You might also want to visit a Christian bookstore and ask the staff to suggest some reading material, both for yourself & mom, and for the girl and probably the boy-- again, from within the doctrinal comfort zone of the boy. There is a lot out there on chastity and waiting until marriage.
The material Burke provided above is very accurate and very serious. From the Christian view, it is as much a spiritual wrong he has done her as any other kind. A book and resources (maybe other kids in the same boat) about "second virginity" might be in order as an option, especially if either or both of them begin to get a sense of what they have done to themselves and one another.
I think it's highly unlikely you will get a chance to make any headway with the boy on the gay issues. I take your description about that not as a sign of how he feels about that per se, but as a sign of how Evangelical is his bent-- a sign of hope in this case more than a concern, IMO, since the Ev's are pretty committed to the rightness of saying NO till marriage, and teaching kids that.
Also, what about the boy's family? Does the girl's mom know his family at all?
In any case, it is not required that parents have the permission of their children to enforce closer supervision. This girl may be very relieved to have that expression of adult caring and structure. Dr. Phil actually has a great approach about this issue-- which is, mom can say, "I do not even need to know the details. I know enough about what is happeneing that we just aren't going to go there. Instead, here's how things are going to be: xxxxxxxxxxxxxx." And then she would lay out what the ground rules are going to be to keep this young lady safe.
Somewhere on the hard drive I have a one-pager about how one can tell a person is actually and sincerely repentant. It's about an increased sense of personal accountability-- not guilt. Please PM me if you want a copy of this.