I am a little late to this post, but better late than never.
I think that the odlest medical college in the South was the Medical College of Virginia, which was then (and is now) located in downtown Richmond. It continued during the war, with an abbreviated course of study. The second oldest, I believe, was the Medical College of South Carolia, founded in the mid-1820. By the late 1850's it was graduating about 100 physicians annually, many of whom came form outside of the State. It was located in Charleston.
The Medical Colelge of Georgia (Located in Augusta) was founded in the mid-1830's, and its graduating classes by the late 1850's were clsoe to 75 per year. I am told that there were small pre-war medical college in Savannah and Atlanta, but I do not know the names.
The Medical College of Lousisiana was one of the earlier school in the South, but I do not know the date of its formation. There was a small medical college in Gavleston, Texas, which was founded in the mid or late 1850's.
I am almost morally certian that there was a medical college in Nashville, but I can't recall its name. I would suspect that Mississippi residents would would have gone there if it was in operation.
The oldest medical college west of the Blue Ridge, and one of the most prestigious in the nation, was Transylvania Medical University (or College), in Lexington, Kentucky. It had been in exsitence since I think the late 1820's. The office of alumni relations sent me a print-out of the students who were enrolled there through the 1860's, and then after using it for my limited purposes, I gave my copy to a local genealogical society. I recall that many of the student body came from areas of the South in the Mississippi Valley. Some time after the war the medical school was absorbed into the Medical University of Kentucky. I am sure that a number of Mississippi physicians were graduates or attended the school.
I seem to recall that there was a medical college in Maryland, which may have been the forerunner of Johns Hopkins.
The two most popular Medical schools in the North for southern students were both in Philadelphia, the University of Pennsylvania Medical University and Jefferson Medical University, both of which are still in existence today. At one time more than one third of the student bodies of those schools came from below the Mason Dixon Line.
I am making this an extraordinarily long post, but will plow on. My great grandfather was a doctor, graduating from the Medical College of Georgia in 1858 or '59, I forget which now. The family "lore" was that he was a "Confederate surgeon," but there was absolutely no mention of him in the Compiled Service Records, either among the Field and Staff rolls or the units from Georgia and South Carolina (his home). A county Confederate pension "census" (for lack of a better word) listed him as a veteran, giving his unit as "N.C.," and the family lore again had shown him serving with a North Carolian unit, which not only made no sense, but he doesn't show up on the rolls there either. Just by happenstance I was going through the amnuscript records of the Secodn North Carolian Hospital, which was located in Columbia, S.C., anbd he shows up all over the place in them. Apparently he got conscripted in `1863, but his heallth was too precarious for field service -- its a wonder he was living, then -- so he was assigned to the Second N. C. Hospital in Columbia as a hospital steward, but their muster rolls got burned after the war. The upshot was that he was a physician and graduate of a Medical School, but he served as a hospital steward. I have found that a fair number of the men who eventually were commissioned as Surgeons or assistant surgeons served for some time as hospital stewards. But there were also a nubmer of officers -- and enlsited men too -- who were physicians prior to their entry into service, yet for whatever reason chose to remain in line units. Part of that was undoubtedly the good of the service, but I am sure that it was the personal choice of many to demonstrate their manhood. And I don't mean that in any demaning way.