I too prefer the movie ending. On a thematic level, it works better. It's a stronger sacrifice for Dr. Manhattan, and it gives meaning to his return. In the book, he basically just returns for Silk Spectre after re-discovering the value of human life. But then he just leaves, because once again he has no reason to be on earth. His final trip away from earth carries little meaning aside from the fact that he now appreciates human life. You could argue that the only reason they have him return at all in the book, on a plot level, is to be there to kill Rorschach.
In the film version, all of that is kept intact, only now he leaves for a reason. To allow the life he now appreciates to continue on peacefully. It's a sacrifice, not a vacation.
Since he is a character who undergoes so much change, and is so complex, I think this new ending which revolves around him more, is far better.
Just my view.
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