It's also my understanding that completing more prereq's can help you move up on the waitlist. If you are currently in any of the prereq's, I would definitely send that transcript in at the end of the semester.
I know that it's a really tough call for you on the microbiology issue. If I were in your place, and this was my plan had I not gotten accepted for August, I would still continue on the path that you are on. I had decided that if I hadn't been accepted, I was still going to take microbiology this summer so that I could be even more competitive to apply for the next semester. It just all depends on how committed you are to MSON. I had all my eggs in this one basket, and I had no intention of going anywhere else, so I would have kept trying. And from what I've read, many people have been accepted on their second attempt. (And that's if you don't get called in the next couple of months.) You are ultimately just going to have to go with your gut instinct. Oh and by the way, I wouldn't hesitate to email admissions with your questions. That's what they are there for, and I KNOW that many waitlisted folks are dying for more answers.