I know these posts are 5 months old, but this thread is still going and
LizzyM posted yesterday so I figure it's not necro'ing to reply to these posts.
Anyway, granted I'm not in med/grad school yet, but I'd imagine the reason why there's so much attrition in MD/PhD programs is because of the apocalyptic landscape of modern science. I think most people going into PhD and MD/PhD programs are aware of the issues of low pay and scarcity of tenured positions, and many are also aware that it's hard to get funding. However, I think that many (if not most) of them are also greatly underestimating the severity of these problems going in, especially the funding situation.
It's one thing to accept a low paying profession with bad job prospects if you can at least succeed as long as you try hard enough/are good enough. It's something else entirely to find out that even if you get your coveted tenure track job that you may still never be able to do research due to the fact that the current success rate for R01's is something like 4-9%. And as if that wasn't bad enough, many universities require faculty to obtain at least R01 in order to be considered for tenure promotion. And if you don't get that R01 within a certain time period of arriving (which is getting more and more impossible as the NIH goes year after year without a budget increase) then you kicked off the tenure track. Even if you don't get kicked off, more and more universities are putting clauses into their professors' job contracts that stipulates the professor has to pay their own salary with grants, which means no grants = no salary.
So it's really not surprising that students see all of this, see medicine with it's extremely good job security and high pay, know that they're already on track to get an MD anyway, and say "**** this" and go MD-only. Even for the students who are committed to research, some are always going to be unlucky enough to get stuck with a project that never goes anywhere, a PI/mentor who dies in a freak accident/illness or changes universities, or anything else that causes their PhD training to take much longer than usual. In that case, combined with everything else above, you'd have to have a superhuman commitment to research to not just cut your losses and change your career plans from "physician-scientist" to "physician".
So I don't really think there's anything MSTPs or the NIH can do to lessen the attrition rates since they're do mostly to the chronic lack of research funding and inherent problems in PhD training. Really the only thing I could think of would be to actually favor "boring" candidates in MD/PhD admissions since the introvert with a laser focus on science is less likely to be bothered by the time demands and setbacks inherent in research training and careers than the social butterfly with several hobbies/interests completely unrelated to science or medicine. But even then I hardly think you'd see anything resembling a large decrease in the attrition rates of MSTP and PhD programs.