if you're doing MD/PhD, do NOT under ANY circumstances go to a school that you don't feel passionate about. if you are going for straight up med school, sure, just suck it up and go to one of your two acceptances. however, a PhD program is completely different.
think about it this way. medical education is tightly monitored by accretation agencies. Therefore, this type of quality control ensures that you will receive an adequate education essentially at any medical school you go to. this is NOT TRUE for graduate school. There are no rules and no standardized tests at the end of a PhD to ensure that you received quality training other than three rickety old professors at the end of your thesis defense. therefore, it is absolutely CRITICAL that you find a department/professor who you truly believe that you will thrive under. plus, with NIH funding being cut right and left, scientists are having more and more trouble getting grants. how are you supposed to train if your lab is dying because of lack of funding? my parents are research faculty at a state medical school, and they say that labs are folding left and right because of the cuts in funding and the inability to convince NIH to fund THEM instead of, say, JHU PI's (who i believe receive the most funding). therefore, if you have to spend another year trying to get into X lab at Y medical school which you really really really want to be at, then go for it.
also, whoever said that 'labs are all the same' clearly has not done research. coming from different labs (even if it's the same area) means that given the same problem, two people will think about it differently. this clearly matters a LOT, if you're trying to become a scientist.
finally, i don't believe that medical school applicants really have an accurate idea of what it is like to do an MD/PhD. it's not just challenging academically. it's a freaking marathon mentally and physically. you're going to spend the ENTIRETY of your 20's at ONE institution. med students will be done (most) at age 26 and you will be 30! this decision is extremely difficult, and do NOT let anyone pressure you into taking a position that you don't feel strongly about. it's hard enough getting through an MD/PhD WHEN you start the process giddy with excitement. i mean, how many MD/PhD's at the schools you were interviewed at said essentially 'i'm DYING to finish asap?' and some actually drop out.
sorry for being so long-winded (and kind of incoherent). it's early and i'm kind of in a rush to the gym....
addendum: but i do agree that you shouldn't have applied to a school that you essentially can't bring yourself to go after you got accepted. that just doesn't make sense...