Hey,
I'm going to be starting in the MD/MBA program at Harvard this coming fall. Granted, there is sort of an "unknown" to it, given that it's the first year, but at the same time, I think both schools have a good grasp on what they do individually. It's technically a "paper program" today, but I feel like that's mainly because it's not off-the-ground yet. But talks for starting this at Harvard have stretched back several years; it's not something that's being done over night.
I've spent a lot of time speaking with the head of the program, and here's what I can tell you about integration. There will be specific coursework -- classes and seminars -- over the first three years that are geared towards the MD/MBA students, known as the "Health Management Seminar" experiences. There are a ton of MD/MBA faculty members spread out across Harvard's teaching hospitals, and they are recruiting a lot of them to help serve in the program. The two schools are also working together to create a series of summer experiences that allow students to get exposure to both "medicine and management" -- including a hospital rotation focused on health care management.
The other thing that's important to note is the way that the MBA is structured at HBS may be slightly different from other schools. The first year is entirely RC (required curriculum), meaning that all 900 people in the class take the same 5 courses each semester. The second year is entirely EC (elective curriculum), wherein there are probably 900 different schedules that people end up with. Harvard also has some really great faculty at the Business school dealing with healthcare management and related issues who already offer courses and guide fieldwork in these areas; I'm sure within 4-5 years they'll only be expanding.
All that having been said, I agree that MDs probably have a LOT to learn from B-school without additional course offerings. Additionally, there are several paths to an MD/MBA -- (1) an integrated joint program; (2) starting med school, taking time off for b-school at the same institution, and then returning and completing med school; (3) starting med school, taking time off for b-school at a *different* institution, and then returning; or, as is the case for a bunch of MD/MBAs I've shadowed (4) going back and getting an MBA several years out of med school (post-residency). I think all are viable options; the thing that appeals to me about 1-3 is that you have the management training from the onset; the appeal of #4 is that you have experienced the work-place for a significant amount of time and probably have a broader context within which to understand the material presented in b-school. The one caveat is to look into application timing -- Harvard requires you to apply to both schools separately and simultaneously (they're really hoping for 5 years of integration); Tufts makes you apply at the same time, but you can simply apply to the med school and check off the MD-MBA option on the secondary (and write an extra essay); many other schools encourage you to apply during your second or third year of med school.
To the OP -- It's good that you're starting to look into these things early. Best of luck, and feel free to PM me if you have questions! For me, I knew going in to the process that the primary factor was the quality of the medical school (based obviously on my own preferences and biases) because at the end of the day, I want to be a practicing physician (I'm *definitely* planning to do a residency) and my medical training is what I care most strongly about. Depending on what you want to do with your MD/MBA, clearly you need to weigh the pros and cons of each of the options individually when you come to them