You really shouldn't dwell on that kind of stuff and think about it. Even if they invited you back and it isn't really normal, the ADCOM has already made their opinion known: they waitlisted you. I'm not saying that to be mean, but to point out that all that other fluff and crap they tell you (or anyone else, for that matter) to make you feel good about your chances or lead you to believe that you have an inside edge is just a charade. The only way you'll know that an ADCOM likes you is when they give you an offer of admission. If not, then they just didn't like you enough.
I said it before and I'll say it again: I think a 2-year masters program would benefit you much more than a 1-year SMP. The way I see it, a 1-year program (whether it's SMP or post-bacc) is designed to just keep someone in an academic setting while they're biding their time for another cycle. You however, are not in that case. Your science GPA is low (which I'm sure you already knew), and now you've even been relayed that info from an admissions officer. I don't know how your GPA is broken down by semesters, but if you're only a year out of college, then you need to show a considerable improvement in performance and commitment to your education. The way I see it (and the message you seem to be getting relayed to you), a year isn't going to cut it.
You were told to do a 2-year masters, so do it. You're young. Another year isn't going to kill you. Why would you risk doing a 1-year SMP (where a single B will have a much more drastic effect on your GPA and a C will kill your chances outright) just so you can try and hope to squeak in your next cycle? What if you don't get in? You'll probably REALLY wish you had gone the 2-year route. Besides, as far as planning for your future, if for some reason you don't get into D-school, a real masters will be of more use to you than just a 1-year SMP certification.