if you are serious about med school, i agree with your advisor - you need to prove yourself in terms of grades. the 3.9 is great, but working on your statement that the program was not rigorous, that means you need to do well on the mcat and nail this post-bac. it's a great opportunity and your research and ECs seem to be really strong - a lot of med schools would be glad to have you as long as they were sure you would work hard academically. it's hard to bounce back from a 2.8.
it sounds, though, like you aren't sure about leaving your research. if you love it as much as you say, you could keep heading in that direction without going to med school. there are a lot of ways to go. just a thought, b/c that seems to be something you're passionate about - the low grades may be a red flag that med school isn't what you really want? when and why did you decide you wanted to be a doctor? before or after undergrad?
then again, i've never met you, i don't know anything other than what you posted here, and i'm not going into psychiatry.
my only real advice is to consider your other options, not because you can't do it, but because if you are reluctant to leave your work for one year, you may find yourself regretting all the time med school will take from your life. if med school is absolutely what you want, then the post-bac will be better than random classes, and make sure to study very hard for the mcat.
good luck!
