If anyone remembers correctly, in Captain America: The Winter Soldier, Natasha Romanov asked Steve Rogers if he would trust her to save him. In which, his reply was yes. Now, when Civil War happens, I'm thinking that he may ask for her help and bring up this fact that she said she would. Which may or may not lead to them having an argument and forcing her to side with Tony, therefore the storyline would go off of the comic books.
However, in The Winter Soldier, they're partnership brought them closer together and their faith in one another increased to where they'd both die to protect each other. So here we have the possibility that she will in fact side with Captain America. After all, she had worked as a PA to Tony Stark in Iron Man 2 and in pretty sure we could all tell what she was thinking at any moment.
Thats just my opinion and thoughts but I could be correct.