While I would be among the first to encourage people to pursue their interests, finding MSTP programs that support non-traditional Ph.D.s is a difficult task. Neuronix brings up several important factors to consider. It wouldn't be fair to tell you that you won't face resistance, because it wouldn't be true. There are some programs that do support and even encourage students to pursue PhDs in non-basic science fields. However, this seems to be the exception rather than the rule. Therefore, if you are interested, you need to find out from specific programs about their take on the whole issue.
That all being said, we definitely need an increased number of physician-scientists in non-basic research fields. There is a lot of translational work that needs to be done, and this requires physicians from a multitude of perspectives.
One thing you should keep in mind is that your choice of PhD work does not necessarily dictate which medical specialty you will pursue. For example, you could do research in the basic biology of psychiatric disorders, but then become a practicing neurologist (or a cardiothoracic surgeon for that matter). The goal of the graduate school part of an MD/PhD program is to give you formal training in how to think about scientific problems, ask questions, and develop ways of tackling them. Therefore, it really doesn't matter what area of research you pursue for the PhD, as long as you acquire the know-how of being an investigator.
In addition, you should realize that what you get your PhD in does not necessarily reflect the area of research in which you were involved. What you get your PhD reflects more the departmental structure of the institution which you are attending. For example, at UCSF, you could do the Neuroscience, Tetrad, Biomedical Sciences, or other graduate programs and still work in a given lab, with the caveat that the lab must be affiliated with your program. Many labs here do, in fact, have multiple affiliations, and therefore you are free to choose the graduate program based on other factors. For instance, there are many faculty in the psychiatry department doing research on things like schizophrenia, BAD, and other disorders, who are affiliated with the Neuroscience graduate program.
Hope this helps. 😀