Over on his tumblr account, Neil Gaiman was asked the following question by harryhadouken:
Is the War Doctor now considered as the canonical Ninth Doctor?
I'm not sure why Gaiman would be the one to ask this, yes he has written The Doctor's Wife and A Nightmare In Silver, but does that make him the authority on all things Who? Either way… the writer gave a pretty good answer:
I don't really understand the question. I'm tempted to say something like, "No, the John Hurt War Doctor is just something that happened in THE NAME OF THE DOCTOR, THE NIGHT OF THE DOCTOR and THE DAY OF THE DOCTOR on television."
If it happens on the TV, it's canonical, unless it isn't. (For example, no-one seems entirely sure whether we get to see pre-Hartnell regenerations during the mindbending battles of Brain of Morbius.)
We now know there was a regeneration between the Paul McGann Eighth Doctor and the Chris Ecclestone Ninth Doctor, one whom the Doctor himself has only just begun to regard as being The Doctor (as opposed to being something else).
If you mean, "Do we now all have to agree to renumber all the Doctors?", I think the main purpose of numbering things is to communicate, and we all know who we mean when we say Doctors NIne, Ten or Eleven. If anyone corrects you and says "You mean TWELFTH!" when you say "Matt Smith was the eleventh Doctor" then that person is being irritatingly pedantic and should be pitied, in a nice way and with a gentle friendly, not-patronising sort of love, because they will have long hard lives ahead of them.