Don't be afraid to set boundaries. As long as she's under your roof, you are responsible for her, and she needs to respect your decisions. If you are exercising good parenting, you are not making decisions to make her "miserable" but rather to ensure her safety and well-being. Remember that everytime you imagine she will sneak behind your back or be disobedient.
Enabling bad behavior in the long run is worse, and she will come back to you one day with a blaming finger when she gets an unspoken okay from you to do things that she may not be ready for, because you wanted to avoid confrontation, or feared she'd keep things from you.
Please do not take offense, but I think you are allowing too much with these two. Even though everything seems to be happening on your turf, it seems the boy has the upper-hand the way I see it.
So far, you allow him to monopolize your daughter's prime free time on weekends (8 hours is an awful lot for someone who isn't anywhere near finished with school, nor has a career plan, and probably isn't making plans to marry her, buy her a house, and raise her kids), you've allowed him to go into your daughter's bedroom, you've told her that if they want to have sex to come to you, and you'll get the "supplies", by bringing everything to your house, you've told the boy, his parents, and your daughter that not only do you condone anything (good or bad) that comes from this relationship, you are also going to take full responsibility for it. Afterall, where are this kids' parents in all of this? Have you talked to them about how "they" feel about sex, and if these two wind up with kids or derailing their education because this relationship has gotten too serious, too soon?
Offering to take her to the doctor is often a "green-light" to many teens, and to the surprise and dismay of many parents, the very thing they're hoping to avoid happens shortly there-after. I wouldn't be surprised if they've already beat you to the punch. When I was a kid, my friends whose parents took them to the doctor at age 12 (as soon as they started menses) started having sex shortly thereafter...and one friend was so irresponsible about using the supplies she wound up missing graduation because she was going to deliver at any moment. The boy didn't marry her, though they were "sweet-hearts" through high school. She gave the child up for adoption and he wound up marrying some debutaunte and pageant princess from Alaska.
This friend's father was shamed (they came from a family where many of the buildings of a particular University and another local college bore their name.) and she was disowned and went through a lot mentally behind the whole thing. She never went to college as she spent her entire high school years investing energy into this puppy crush that went no where.
I say you feel uncomfortable because deep down inside you know allow these two this much freedom is a mistake. They are not emotionally ready for this. If I were you, I'd be encouraging my daughter to make the most of herself during these years by excelling in school, finding who she is and what her strengths are through worthwhile hobbies and activities, and by spending more time you with and your family bonding. She'll have her whole life to find her special someone when the time is right and she's accomplished.
I think serious dating during the teen years is over-rated. I know money is tight, but there is so much out there for young women today that is so worthwhile for character building. Allowing her to put so much focus on romance, and hormone related endeavors will do nothing for her self-esteem let alone teach her how to make worthwhile decisions in the future. The only life-skill she may get out of this is heart-break, pregnancy, mental health issues, and even a disease....and all before she graduates from high school. Not only will you have to suffer along with your daughter whatever the outcome may be, you will also have to live with knowing you had a hand in allowing her to make these bad mistakes. Get a spine and get tough. Set this girl on the right path for own good and yours. Tell her and this boy to get a life.
Don't serve her up on a platter to a kid who may be nice, but probably isn't worth the trouble. Gently guide her to invest in herself and maintain a friendship with this guy. If he's the one, he'll wait or be back. That is my opinion.
As for rebellion. If she fights back let her. Then her own hard-headedness will be to blame and she'll know she only will have herself to blame. YOu will know you're doing the right thing setting real boundaries and give her clear concise reasons why. In the end she WILL respect you for holding your ground and setting a good example.
My parents did this with me and while I didn't like it then, and fought them a lot of the way. I am so happy they did. And I respect them.