Okay, I’ll jump in.
First of all, good for your girlfriend for losing the weight!
I started with Starting Strength and I liked it. (read http://startingstrength.wikia.com/wiki/Starting_Strength_Wiki and eventually get the book.) Some people around here like The New Rules of Lifting for Women. As I understand, 5x5 is also a legit beginner’s program. There are a lot of options, but she needs a beginner’s program that’s mostly compound barbell exercises, assuming she can handle the bar. If she’s starting off very weak, she’ll need to substitute lighter dumbbells and/or bodyweight exercises. The main thing is to keep increasing the weight. Low weights/high reps do not “tone” (and in fact we tend to frown on that word around here, though I know what you mean.)
Cardio? People are going to disagree on whether it’s necessary, but I think it’s at worst harmless. The key is, it shouldn’t be all she does. And she shouldn’t run before lifting.
Also, show her stumptuous.com. Very refreshing attitude, much better than most exercise information aimed at women.