If you are not opposed to going the DO route you could repair your GPA twice as fast by retaking the pre-req courses in which you received worse than a B (3.0) (capitalizing on their grade replacement policy).
If you are adamant about pursuing an MD then it would be in your best interest to stick to new upper-level science coursework. Since MD schools don't participate in grade replacement, a 3 credit gen-chem class will simply be added to your transcript, along with a retake 3 credit gen-chem class or a 3 credit immunology course (or any subsequent coursework).
I've heard (though this is simply hearsay) that AdComs are not terribly impressed by applicants who retake pre-reqs after they've taken a bunch of upper-level classes because they're no longer on a level playing field with the people who have no background knowledge (so it's less of an apples-to-apples comparison).
However, if there are pre-reqs in which you received worse than a C (2.0) then you must retake them, as you would be required to do so by all med schools. A 3.0 cumulative GPA is a decent benchmark to consider yourself ready to apply to SMP programs (as that's the cut-off for many programs).
