Alright, with fear of insulting someone, here is my 2 cents:
I think everyone is blowing this whole Stanford probation WAY out of proportion! Although it is nice that we now have the facts straight, the truth of the matter is that many "so-considerered" scientific powerhouses- Harvard, UCSF, Columbia, and now Stanford (to name the ones that I know of)- have been placed on probation in the recent past. However, the truth of the matter remains that these places are all still AWESOME places to do a MD-PhD... This just speaks to the ever-present complexity of merging clinical medicine and basic science, and the fact that the NIH made have a single ideal for a MSTP program. I don't know about you, but some of the programs I visited this year that were supposedly "ideal" MSTP programs weren't for me.
I would further argue that the MD-PhDs and MDs I have met from Stanford are some of the most inspired scientists that I have ever met. My current advisor did some of her training there and speaks very fondly of her time there! Stanford just had a change of directorship for their MSTP this year, and I think NIH-cited problems will be quickly addressed. Further, by examining the names of the schools that have recently been placed on probation, I would say that the extra attention that had to be placed on these programs to retain NIH has made for wonderful progress in their organization.
So, why not go to a place that may be receptive to change and that you can be a crucial part of shaping MD-PhD education? Stanford remains an excellent choice for your training... I would jump at the opportunity to attend... unfortunately, I didn't receive an interview.
Plus, the scientific community in N. California... Coupled with the weather, who could ever ask for more??