Hi there,
I will be doing my PhD at Emory in epi. I interviewed a lot of places, and was uniformly open about my intent to do my PhD in epidemiology. Two places received me with open arms and enthusiasm - Emory and Minnesota. Both great public health schools, Minnesota is stronger (at present, though they are evolving to have a broader focus) in chronic disease, Emory in both infectious disease and cancer. I'm interested in ID, so Emory was the clear winner (and you can't beat having CDC next door!) Minnesota has one (or two? I can't recall) students in epi from the MSTP program, Emory has three (including me) and has been actively recruiting more this year.
I have found it wonderful to be at a school that embraces 'non-traditional' MD/PhDs. I have spoken with other MD/PhDs in epi (at other schools) that entered through the 'backdoor' - stated an interest in neuroscience or some other more traditional science such that they could switch to epi once they were accepted. I don't think I would recommend that, particularly since you will have a better experience at a school that will support your research interests off the bat.
Feel free to email me with any questions - I'm happy to encourage more people to consider this option!