First, I'd like to clarify a few things. Looking at the average time to graduation of a specific program can be misleading because of the small sample size. Everyone has heard the horror stories of the poor student taking 10, 11, 12, etc years to finish an MD/PhD program. It is funny how these stories start with a couple of exceptions and then get multiplied, magnified, and highlighted until they become legend and eventually mythologized. (This phenomenon, among other things, is called availability bias).
The students who have taken an unusually long time often have experienced personal difficulties, taken time off, had their advisor leave the school, taken on a project that takes a long time, or taken on a project that wasn't very well-designed (i.e. spent years and got negative results). Obviously, some of these variables are within your control and some are not.
I think the key is to get focused, be self-motivated, and carve your independent path toward your goals. One specific thing to do is to look for programs that have built-in flexibility and ways of reducing unnecessary requirements. Other methods that will help you achieve your goals as an MSTP student include planning your time well and being productive no matter what you decide to tackle.
Honestly, I can say that as an applicant I was worried much more than I am now about time to graduation. The thing you realize is that there is so much to learn and that you are actually getting paid for it! There will be no other time in your life like it. Moreover, I have realized that it is important to have a life outside of medical or graduate school during the program, and to not wait until afterwards. There are some great examples of people who have gotten married, had kids, and taken time off during the program.
In summary, I don't think that the time to graduation should be a major obstacle to accomplishing your goals if you really want to do both medicine and research.