I don't think a med school would frown on someone enrolling in graduate school in a gap year, and may even smile up them, if it was clear they would finish and that they would enjoy/benefit from the program. I mean, if you don't intend to FINISH, then they SHOULD be upset. But if you are all set to finish before matriculation, I don't see what the problem would be.
BTW, I am in a very similar situation. I am enrolling in a program that nominally takes 2 years, but that I could accomplish in 1 year + 1 summer (before matriculation). My reason for going is an interest in the subject (physics), availability of courses in medical physics, and that this particular program is all paid for (with livable stipend) by a TA job.
I had considered taking another year to really get a full experience from the masters, but I'm hankering to go to med school sooner than later. I had also considered similar options (apply now or later or defer) but never considered NOT finishing.
OP: I would guess that if you are definitely not going to finish in one year, then wait to apply. If you think you might, then you could apply and give the impression that you would finish. If you can't make it, you could defer. I would guess that going into an application season looking like you are going to defer would be a big drawback though. BTW, any hints as to what type of program this is? I would guess that if you could angle it towards helping a career in medicine, it could HELP your application.
Question: Is it then up to the applicant to say "hey, one year and done" or will the med school just decide that this person should be taking two and subsequently not accept them? Just a thought...