There wasn't that much difference between the novel and the movie. Really, the only difference is that instead of both of them writing their memoirs (so to speak), only Amy does this. The fact they stay together and she is pregnant is identical in both works.
Quoting from the Independent:
In the run up to the premiere, Fincher quoted Ben Affleck as saying of
Flynn's screenplay, “This is a whole new third act! She literally
threw that third act out and started from scratch," but the author has
since played this down, saying the reports following it were "greatly
It seems the original basis for this story was that Fincher was disappointed in the box office reaction to his faithful adaptions of The Girl with the Dragon Tattoo and so supposedly wanted to change the ending. Given Flynn's comments above, it seems likely that these sentiments were either misinterpreted, or never true to begin with.