I'm assuming you're talking about BU (there are other MA in Medical Sciences programs, Loyola is an example).
I don't know if I'm reading your post correctly. But if you're saying that you're going to apply AFTER you get your first semester grades, that is really, REALLY late. Not a good idea.
If you're filing AMCAS this Summer and doing the MA in Medical Sciences program this Fall, that's cool. You can also try and finish most of your secondaries since BU MA in Medical Sciences doesn't start till September. I wouldn't apply during the program if your GPA is pretty low, but it's probably fine if your stats are borderline (e.g., 3.4 cume / 3.3 bcpm / 30). If you want to make sure the adcoms see your performance in the BU program, then apply after you have one year of coursework on your transcript.
BU GMSers can correct me on this, but you can take public health courses as well as GMS courses while you're doing the MA in Medical Sciences at BU. One of the cool things about the BU program is that you can get an MA in Medical Sciences and an MPH in two years (could be expensive though). Maybe you could even do it in less if you take some Public Health courses while enrolled in the MAMS program. I think this is a strong aspect of the BU program and BU's public health school has a solid reputation (US News Top 20 if their rankings mean something to you 😀).
