Salt has two different endings because of Noyce's different opinion from the producers' and studio's. From Wikipedia:
Director Phillip Noyce has said that due to the extensive usage of
flashbacks, "there was always going to be a mountain of alternative
material that would not fit into the theatrical version." The film
ended up having two extra versions, the Director's Cut and the
Extended Cut – which Noyce refers to in his audio commentary as the
film's original cut – both included on the DVD and Blu-ray Disc deluxe
editions.
The Director's Cut was described by Noyce as "my own personal take on
the material, free from the politics and restrictions of producers,
studio or censorship ratings." Four minutes of film are added,
leading to a running time of 104 minutes. More flashbacks are
added, and the violence is amped up – for example Mike being drowned
rather than shot to death. The ending is also different: in the
bunker scene, Winter shoots the President instead of only knocking him
unconscious, and a media report during the final scene reports
that the new US President had been orphaned on a family visit to
Russia, implying he is also a sleeper agent. Noyce has described
this ending as "an ending yet just a beginning – and it's an ending
that turns the whole story on its head".
On the side note this film has three versions:
- the Theatrical version (100 minutes),
- the Director's Cut (104 minutes, plus changes to existing scenes), and
- an Extended Cut (101 minutes, including the removal of some scenes and a different ending). - (Source:IMDb)