I'm not going to claim to be the world's biggest expert on Wolverine or the Marvel Universe, but I do know enough to know that Wolverine has several backstories, many of which conflict with one another in minor ways.
The relationship between he and Sabertooth was always hinted at, but wasn't always canon law.
I remember in my comic-book reading heyday back in the 80s and early 90s, it wasn't obvious that they were brothers. It's a great plotline, though and I'm glad they pursued that angle in this movie.
People need to realize that these are stories (and always have been) and it's not like there's a definitive and absolute history that goes along with these characters.
As long as someone's telling a good story and keeping the character's essence essentially intact, what's the harm of taking some creative license?
The writers of the comic books themselves have always done this and have been more than willing to bring a character back from the dead or write around past history by creating alternate universes etc.