If you want to go to medical school, what's going to matter the most is getting a strong background in logic and having a high GPA. I don't know if MIT or CMU has more grade inflation, but that should be a major factor if you can figure it out. MIT also has a really strong math department so they might offer more rigorous logic classes that will help out with the MCATs.
But with all that said, if your smart enough to get into MIT as a transfer, you'll have no trouble getting into medical school. Go where you feel most comfortable.