I'm still trying to make sense of the ending.
I don't believe the doctor took her. For one thing, I don't see how he could have possibly taken her out of there without anyone noticing. He also didn't seem like the type who would do something like that. (But you never know in this game.) Then again, could have had the tools at his disposal to drug her, I suppose.
That leaves the guy on the radio. My guess is he told her to come outside without being seen, luring her outside. She may have even gone with him willingly, if he told her that he knew where her parents were (not likely though, given the blood on her hat.)
The only problem with this is it does not explain the doctor's disappearance. Perhaps he witnessed the abduction and elected to follow them, but why not alert the others?