The fact that Scout never sees Boo again gives a sense of closure to the ending. The book started with the kids wanting Boo to come out, he has, and now he can go back inside.
It also gives Scout a secret, a special surprise, that she doesn't have to share with Jem and Dill. For all of the times that they insisted she couldn't play with them because she is girl, she was the one who got to see Boo Radley.
Lastly, it would be unlikely that one event would cause Boo to make a sudden switch in character. Though slightly sad that Boo goes back, Jem makes the observation earlier that Boo wants to stay in his house. Boo made the choice to come out to save the kids and he makes the choice to stay in the house again. He isn't being kept there against his will.
A large part of Scout's childhood revolved around the mystery of Boo Radley. While she was a child, she remained innocent; she did not understand why Calpurnia's church only had one hymnal--because she was blind to racism--and she did not understand why people did not believe Tom Robinson. Throughout the book, however, as her "relationship" with Boo progressed, so did her understanding of how the world around her operated. At the end of the novel--when she was saved by Boo and Tom Robinson was killed--she lost the innocence of her childhood. Boo Radley represents, in part, innocence, and when she lost her innocence he disappeared out of her life.