As for the rape scene - I could definitely have done without it. I don't think it adds any more to the story to SHOW it than it would have if it IMPLIED it - in fact, it would have left it up to the imagination of the audience to imagine what he did to her. The worst part of it is that it doesn't build anything into Salandar's character - it doesn't send her into a depression, and neither does it send her crusading for her own rights - it's a speed bump in the road for her. Even in the films where they had a chance to show how it affects her character, they blew it.
Again, the scene plays heavily into what happens in the second two books as a plot device. As to whether it should be shown - that's really an artistic choice on the part of the director. I would argue that the brutality of the rape is necessary to understand Salander's character, and the nature of her revenge.
When Bjurrman first assaults her (the, ahem, BJ), her reaction is to take a camera with her next time so she can get some power over him, and blackmail him into leaving her alone.
The brutality of his second attack is unexpected to Lisbeth and the audience, and her revenge shows us a lot about her character - she's smart, resourceful and downright dangerous. Up to that point we've seen her as an aspergersy outsider. Now we know she's a force to be reckoned with.
It also gets us to root for her. The revenge she takes on him looks downright psychopathic if we don't see what she's been subjected to.
Later on in the trilogy we discover that Bjurrman's abuse of Lisbeth closeley reflects the treatment of her mother by her father, leading to an extreme act of violence in her childhood that creates her whole pathology.
It also leads to Bjurrman's hatred and need for revenge againsts Salander which is the basis for the events of the second book.
The director could, of course, have watered the whole scene down, shown it off camera etc, but that would be diluting the stories and the motivations of the characters.
Bear in mind that the Swedish movies were created as a TV miniseries that adapted the whole trilogy, and Fincher wants to adapt all three. The scene pays off far more in The Girl Who Played With Fire than it does in GWTDT.