With a mythos as wide and varying as Doctor Who explores, I'm sure it will be easy for them to explain new Doctors in new series until the end of (real) time. It's kind of like the reboot of Star Trek with the new young cast. A time travel/space anomaly event changes the space/time continuum and now a new history is told.

Sadly, I hear Amy Pond will not return for season 7 of the show.