I don't think you're completely finished. Just explain the situation honestly on your amcas app. as Lizzy posted earlier. Assuming you get a decent mcat score and apply broadly, I think you'll find a few adcoms that won't blow this out of proportion like most of the posters here. (this is assuming the situation is as you've described it here)
Maybe.
Then again, it's not in the best interests of a medical school admissions board to take chances on people when there are fifty other qualified applicants who didn't admit to stalking and harassment. There is very little incentive for a medical school to really dig into this issue at all or give her the benefit of the doubt.
So while there IS a possibility that she will find a sympathetic ear somewhere, it's up to her to decide whether or not it's worth the hundreds-to-thousands of dollars to apply and find that person.
And even if she DOES find the person who for some reason can justify the time and energy to investigate this kind of an academic charge instead of just moving down the list, the best thing that she can hope for is to then be put on equal footing with the rest of the applicants (at this one school).
That's not to say that she has a good excuse for what happened. Being given the chance to be heard doesn't mean that she's going to be able to say anything that can save her from the red flag. I highly doubt that most scientists are going to accept true love blotting out critical thinking and good judgment as justification for stalking and harassment.
I agree that medical school is not an impossibility for her, but it's going to require several things to line up perfectly.
1) She isn't auto-rejected for the red-flag.
2) She has a good enough application to not be rejected due to the red flag.
3) She finds someone who is willing to believe there's a side to the story that can redeem her.
4) She tells a side of the story that somehow redeems her.
5) Her red flag is ignored by the admissions person.
6) She has good enough grades to get an interview.
7) None of the interviewers hold the red flag against her.
8) Her interview and application are good enough to get her an acceptance.
Hmm...