How confident are you in your ability to succeed at Gtown? I think that's one of the most important things to consider, though it might be hard to know. The GT SMPs are graded curved against the med students - you have to be in the top 10 to 15 percent of the med school class to get an A. Yikes. I honored med school classes at UMDNJ Newark..........along with like 30 to 40% of the med school class (anyone who gets over 90% gets honors). If you get B+'s or B's at GT you're impressing nobody and the SMP might not help you (it might even hurt you).
There is a flip side to this, of course. Lots of people do well GPA-wise at UMDNJ so it won't distinguish you as much, though I would say it shows your competence in the basic sciences and eliminates that as a 'reason you couldn't succeed in med school' if your undergrad science grades aren't up to par. If you do well at GT i'm sure it would be much more impressive and it may open up avenues at more schools.
When you say you're applying right before starting the program - I hope you're not waiting until late August to submit everything for your app. What I would do if I was in your situation: apply as early as possible, get a 4.0 the fall semester in whichever program you choose, and write update letters at the end of that semester so that your SMP actually enhances your application in some way.