Question: Salt has been with the agency for a long time and has earned the trust of her colleagues, so when she is accused of being a spy, why would her superiors take the word of a defector over her?
Question: Once Salt escapes from the police car (approx 1/2 way through the film), she grabs a fur hat. In the next few scenes she is wearing a matching wrap, including the same fur. Where did she get that?
Answer: She stole it as well.
Answer: They have to at least investigate that kind of an accusation, and when Salt so vigorously resists arrest it basically confirms, in their minds, that she is in fact a spy.
Phixius ★
I actually kind of find it shocking that they would be willing to believe a guy who would do or say anything to save himself and since Salt was with the agency a long time, they could have at least given her the benefit of the doubt.