It's really only one more year, really. Either you work for a year and apply in the fall, or you attend ND for two years, apply in your second year, and go on to your PhD. So you really only "lose" one year--and it's a fully funded year you can spend on research and networking for your PhD and career. I say go to ND.
I had a 3.8 in my UG and both M.A.s, so there were some B's in the mix every time (except my last MA-only A minuses there). I'm starting a PhD at Duke in the fall. My professors told me a thousand times not to worry about the occasional B and I never believed them until now. Seriously, it's not that big of a deal--just take the B and move on.
I have two M.A.s--one in biblical exegesis and one in theology. I think it gave me time to really develop my research and writing style. I think it all comes down to the writing sample.
Well, I was told there were two biblical studies spots, and I assumed that meant one NT and one OT. But it looks like an NT spot was claimed before I turned mine down...so maybe their first choices this year were both NT students?