You've got legitimate concerns. A two week trip is no place to learn to backpack. Even if she was extraordinarily fit, this would be a bad idea without at least a few weekend overnights beforehand, and preferably a trip of at least 4-5 nights so she could get a feel for what hiking with a heavy pack really feels like and what kind of gear she needs. That she's not as fit as the rest of you just makes her situation worse.
Tell your friend you're worried it will be too difficult for his girlfriend since she's an inexperienced hiker, has never been backpacking, and is less fit than the rest of you. I'd put the concerns in that order.
Then propose a solution. If she can prove her fitness and ability to keep up, she can join you. Go on a very strenuous all day hike with the two of them, or arrange a moderately challenging one or two night trip with them. Make it clear that to do the difficult trip, these short trips need to be easy for her, because the longer hike is doing these for 14 days in a row, no breaks. If she proves that she can do the shorter hike with no difficulty, then she's proved your concerns are unwarranted and she's capable of coming on the trip.
If she's said yes, I bet it's because she doesn't know what she's getting into. This solution has the advantage of warning her what she's getting into and reassuring you if she turns out to be more fit than you expect.