I'm so sorry you're in this situation!! I'm sure you've gone back and forth a lot and that it's a pretty agonizing time of uncertainty :/ Congratulations though on the medical school acceptances!
I will kind of chime in with my own 2 cents and experience, and I'll say that from what I've heard, your MCAT shouldn't be a completely devastating problem for MD/PhD, if that's the route you want (as I see my buddy shady_bb has chimed in as I type this!). My score is actually a lot lower than your current score and while I'm definitely an underdog and it hasn't been easy, I'm hanging in there as an applicant this cycle. 4 interviews from 18 applications, with one of them (an MSTP) that should turn into an acceptance in the next couple of weeks based on my spot on the waitlist. I can't speak for everyone, but I'm very fortunate that this has been my situation.
However, I will add that I think the greater problem in terms of re-applying (MD or MD/PhD, I imagine) is that you've already been accepted to MD programs. I don't want to speak as any kind of authority here, but I wanted to suggest looking into how much of an issue this will be. It's possible that declining an acceptance and then trying again next cycle (if that's one of your options) might set you at a huge disadvantage. From what I understand, at some point in the summer, data become available about everyone on AMCAS, so schools could see that you were accepted to medical school this cycle but then declined. I've heard that declining an MD acceptance and then applying MD again the next cycle shows poor judgment, but I'm not sure if declining an MD acceptance and then going MD/PhD would be the same??? I would just check in on this. You would also be a reapplicant everywhere you applied this cycle, so I'd keep that in mind, too.
Re-reading your original post, I see that you are thinking of applying to PhD programs. I think that would be unaffected by anything this cycle, so you shouldn't have any issues on that end! It would be a lot of work to take the GRE and re-apply though, so I'd definitely encourage you to keep soul searching and see if that's really what you want. Have you also considered taking the MD and seeing if you can somehow incorporate an extra year in them to do research? Maybe there are affiliated institutions, even if there's not an actual department/PhD in what you want to do? Maybe they'll allow you to spend some time working at the NIH, and then you can get a post-doc after med school? Not sure of all of your options here, but I think it's worth exploring!
Sorry I can't give you much concrete help, but I really am wishing you the very best of luck!