I decided during my second year of med. school that I wanted the PhD, so I applied for the MD/PhD program - my school does not have a MSTP.
I did not have a problem because they had fewer than the budgeted number of people in the program. This is the limiting factor. However, the way my school worked was that the MD/PhD program paid for the medical school years while the basic science department/mentor paid me during the PhD portion.
Check with the school - sometimes they will work with you, like taking one less person the next year to let you go ahead. It all depends on the money, but it can't hurt to talk with some people in high places (Deans and Department Chairs).