It happens, though I can't really get any firm numbers on how many do it. From what I gather, very informally, it seems to happen on average to one or so of every incoming class at every school. So it's not common, but it's not rare either.
MSTPs are not allowed to reclaim any money paid to the student. MD/PhD programs that are not MSTPs almost always make their students sign contracts obligating them financially to the program if they leave it. This is one more reason to go to a MSTP. Of course, you will be held accountable for the rest of your medical school education, and who knows what sort of fin aid they'll be willing to give you after that...
Careerwise, I can't see how one would be negatively affected by going purely clinical and into something like private practice. Also, I can't imagine why you'd want to leave the MD/PhD if you were still planning on going into medical research or academic medicine. If you did, leaving the MD/PhD (especially for a MD only) could hurt you by way of recommendations and the sort of word of mouth that gets around behind your back when you're being evaluated. Though, I think alot of PhDs would love hearing "the MD was useless, so I took my PhD and ran". Nevertheless, taking a PhD and foregoing the MD is much much less common than those foregoing the PhD for MD-only. If you really thought the MD was useless, you could go do a post-doc and forego residency.
It's food for thought anyways. I like the idea that the program loses out if I leave. It gives them incentive to keep me happy.