1) When Salt arrives on the barge with Orlov and the other Russian sleeper agents, she is taken downstairs to where her husband is being held. In the theatrical release, they drown her husband while she watches. In the Netflix version, the husband is shot once in the chest while she watches.
2) Near the end of the movie, the President and his entourage are in the underground bunker under the White House. In the theatrical version, Winter shoots the President when the latter refuses to comply. In the Netflix version, Winter merely pistol-whips the President into unconsciousness.