Unsurprisingly, the true details are hard to dig up, but this is nothing new. Pixar has a reputation for major shake-ups during production, see this extract from an article on hitfix.com:
They have the best track record in the business for a reason. They have a carefully managed story department, and they are ruthless during development. They have had several major shake-ups on films, including "Cars," "Ratatouille," and "Toy Story 2," with directors being replaced and big chunks of story being thrown out.
A line from cartoonbrew.com, which first broke the news and continues to cover it, reads:
“The key to their success is reworking and reworking a project until it becomes something great.”
Looking through comments from Pixar workers who had seen the original animatic for The Bear and the Bow, it appears Chapman's intentions were a little more off the wall (for that read 'daring and interesting') and not a guaranteed sell for Pixar - hence the change of director and storyline (and title).
It must be said, though, that this move raised a lot of eyebrows and led to much furious internet debate, exemplified in an article from theWrap.com which includes the opening paragraph:
Pixar reaped a heap of anger Wednesday as the blogosphere accused Disney’s animation house of sexism -- and worse, being formulaic -- for firing Brenda Chapman, the first female director in its history, from “Brave,” a film she had written and nurtured through the development process.