I believe that most schools that have an MD/MBA program have the MBA portion fall between the second and third years, rather than the third and fourth. There's already such a natural split there that it makes sense. However, I don't see why you wouldn't be able to do it between the third and fourth years, which are so flexible anyhow. People have argued that taking time off between the third and fourth years is superior to the "traditional" joint degree path, because you will perform better in your required clinicals (since info will be fresher in your mind) and get better recommendations for your residency. I say "bah!"
Schools that don't have an official joint program should have no problem granting you the leave of absence to pursue a second degree (I plan to do this for a different degree and have looked into it extensively).