Unless you are super-hard-core science and math, if you are committed to pre-med, I would suggest Columbia over MIT. There are large classes at Columbia where 90% of the grades are A. I think you will be hard-pressed to find something similar at MIT. There might be smaller, advanced classes where 90% of the students get A’s, but not large introductory classes where that happens. GPA is extremely important for medical school. Since your standardized test results were good enough for MIT and Columbia, I think that you can expect to do reasonably well on the MCAT, wherever you go. An MIT education might give you a boost on a question or two, but probably not on many. You also need to factor in the time that you will have available for medically related volunteering. If you are taking a very demanding course load each semester, you will have a hard time finding the time for that, and it matters a fair amount for med school admissions.
I think that the acceptance rates are not the best measure of the college to pick for pre-med. This only indicates how well students do when they have reached senior year as pre-meds and are applying to medical school. It does not indicate what fraction of the class entered as pre-meds, but decided not to apply to medical school. Some may have found an area that they loved more than medicine. However, I suspect that some were still interested in medicine, but concluded that they did not have the GPA to make applying worthwhile.
If you are not committed to pre-med, then the considerations become different.
You should see how you feel about the two schools when you visit.
MIT is an excellent school for certain future plans, to be sure. I would not advise it for pre-med, though.