It's a tough one and I don't think there is a black and white answer to it. Like many people have answered before, I would rather she had sex in a safe place with the right protection than have to sneak into some dodgy alley to 'do the business'.
However, I would definitely try to engage in active conversation with her about it, because I don't think anyone should be having sex until they can mentally and physically take care of a child in this society, since that is a risk you take every time you have it. Of course, that doesn't stop people from having it, much like people don't stop driving because of the risk of getting into a car accident, but I feel anyone who is having sex (regardless of age) should be prepared to take the risk.
Which leads on to the next point. Would my daughter be prepared to have a child with THAT guy? If I knew he was a no-good 'bad boy' who was taking advantage of her, I would encourage her to seek a positive relationship rather than a destructive one and I would not want to condone her having sex in her room with someone like that.
In summary, if push comes to shove and she is 100% definitely going to have sex with this guy regardless of what I say, I would make sure she has adequate protection available and I would allow it. That is, provided no one else in the house is negatively affected by it (i.e. younger siblings hearing odd noises).