It depends on how long they want to run with it really. Yes he has three more lives to lead, but the reason they came up with the whole regeneration process was so that they could change actors to follow on the franchise in the first place. Regeneration was an added thing to the charcater by means of getting around different actors playing him. This is Sci-fi they could cheat and say that he can go farther than twelve cycles, or they could go into more detail of other time lords. Wasn't there a time lord who came to the end of his regenarations and instead took another persons body. It may have been the Master I'm not sure. And whether this was in keeping with canon of Who or not is another thing.
The one big problem with Who is staying in canon. Alot of the fandom after the TV series is considered canon and alot isn't, and it all depends on how big a fan you are to say whether its keeping with canon or not.
If the next actor decideds to stick with it for longer than a season, then we'll at least have a future of more than thirteen episodes per doctor. However if the next few actors, like Eccleston think drinking from the poisoined chalice ain't for them, then the writers will have to come up with some sort of storyline in hopes to keep the Doctor going past twelve regenerations.
It seems in a certain way they have kept in canon with the fact that Gallifrey no longer exists. If I remember my homework correctly, the Doctor had something to do with it's demise. I know in the TV show it's been hinted at that Gallifrey was destroyed in war, but that is it. It could be safe to presume it was a war between the Doctor and the other timelords. Or it could be something completely different.
I've been reading through the .
doctor who wikipedia which cleared some things up but then confuses you at the same time. So much stuff to trawl through but a very extensive interesting read into the Who backstory.