As I remember it from the book's ending, Hannibal kept Clarice more-or-less continually drugged and they live happily ever after.
The difference is covered in AboutFilm's note on the ending, in 12 paragraphs and a synopsis of the book's ending. An extract:
Admittedly, I haven't read it, but the
novel's ending sounds just awful to me.
And yet, it still sounds better than the
movie's ending. At least the novel's
ending explores the psyche of both
characters. At least Starling asserts some power, as preposterous as her
therapeutic techniques may sound.
Could it be they just didn't have the time to give the book's ending the full treatment it deserved to be fully explored? Hannibal escaping into the sunset is certainly easier and quicker than working through and resolving their psychological problems as mentioned in the synopsis.
In the movie, Hannibal is Starling's self-
appointed protector and is the same
person from beginning to end. But he's
not the same person he was in The
Silence of the Lambs, nor is he the same
person Harris portrays in his novel, in which Hannibal is not so much trying to
protect Starling as he is trying to get her
in his clutches. In the novel, as ludicrous
as it may sound, we have a
transformation and a resolution. That's
something we have a right to expect at the end of a trilogy. However, in the
movie, Hannibal just flies off into the
sunset. He is still an enigma. We're just
set up for another sequel, and perhaps
another. Don't look now, but Hannibal IX: The Resurrection is just around the corner.
A posting by Lectermate on the Hannibal Lecter Studiolo says:
In an interview, Ridley Scott said about the end of the book that it was too fast, that it should have been another book before we saw Hannibal and Clarice together.
Scott thinks that Hannibal is in love with Clarice but she rather feels some kind of respect for him, that's why he decided to do another end for his film.
To which Clariz replied:
That is what he said in the interview, but in real life, there was a big ado, between TH [Thomas Harris, author], Dino/Martha [De Laurentiis/Schumacher, producers] and [director Ridley] Scott, whereupon TH didn't want to agree to the modified ending.
After they were locked for 5 days engaged in the argument. TH gave in, not without a feeling of disappointment.
What it odd here, is that the book was written with the foreknowledge that it will turn into a movie. When it was finished up and up until the production of the movie began it seemed clear that the book ending would prevail. Dino and Martha had approved it.
It always seemed as if they modified the ending to the movie with the idea of a sequel. Scott definitely had a sequel in mind. One wonders if he actually READ the book or just an abridgment.
There is no substantiation that might lead even remotely to believe that TH wrote the ending of the book to satisfy any fans. That would be soooooooo unlike TH...