In MSTPs you don't have to pay back for the first two years. In non-MSTP MD/PhD programs, it depends on the program. At my program (Dartmouth) you get billed for however much tuition you would have had to have paid but you don't have to pay back the stipend money.
I will say this though: dual degree programs (especially MD/PhD because of the time, effort, and money each school pumps into each candidate, and the fact that the NIH gets mad at MSTPs if their dual degree candidates drop down to just an MD) are not programs that should be entered into lightly. You shouldn't just look at an MSTP as a way of getting free med school. These programs should only be undertaken by people who as sure as possible that what the complimentary degree will provide for them is what they have a passion for. So, if you don't have a passion for research, don't apply MD/PhD. Also, if you get accepted to a dual degree program, that means that someone else who wanted both of those degrees has been shut out of getting them from your school. Yes, most schools will allow you to change your mind and drop the second degree. But, if you decide to go to a school that has admitted you to a dual degree, especially the MD/PhD, you should look at it like a "gentleman's agreement": Sure, you can drop it, but there had better be a very compelling reason and you will be letting the school down.
