Welcome to SDN, Random Numbers and Letters!
My opinions...
In your case, I think it would be pointless to retake prerequisites. The only ones I would consider retaking would be courses that you got a C- or less in. Like you said, your MCAT clearly demonstrates proficiency. I think retaking the prerequisites would probably be seen as regressive. If I were in your shoes, I'd opt for a special masters/certificate program (Georgetown SMP, BU MAMS, Rosalind Franklin AP, EVMS Biomed, Drexel IMS certificate, VCU certificate, etc.). These are intense programs that range from 27-48 credits in one year. 18-24 credits in one year is considered a normal full-time courseload in grad school, so 27-48 is pretty intense. Many of these programs allow you to take courses with the medical students. If your undergrad performance is not representative of your academic abilities, the special masters/certificate programs can prove your worth. Keep in mind, however, that these programs will give you a new GPA, Graduate, on the AMCAS (the US MD application) that will not contribute to your undergraduate 3.3/3.0 GPAs. On a related AMCAS note, your 2 Fs will still be averaged in your undergrad GPA. I'm not sure whether you're aware of that or not, so I thought I'd throw that out there. However, for the AACOMAS (the US DO application) if you retake, only your most recent grade shows up (regardless if it's higher or lower than the previous one).
In your friend's case...Spend 1 year, ~32 credits, taking mostly undergraduate upper-division science courses. This should push her cume/bcpm GPAs to 3.0 territory. I would then do a special masters/certificate program. She needs a postbac/special graduate program to prove that she has what it takes to handle the academic rigors of med school. With her low GPA, Rosalind Franklin's MS in Applied Physiology would give her the highest probability of an acceptance. Even though her MCAT is good, it's not great. But coupled with a solid special masters/certificate program (not necessarily Rosalind Franklin), it might be sufficient.