She could obviously tell that he had a point and that being cordial was the best way to go if they wanted their relationship or better still, their agreement to work out but at the same time, she didn't like the idea of being friends with him.
It's not like she hated him or had anything against him cause if that were the case, she wouldn't have proposed that he married her. Her only issue with his proposal was simply her fear of things not going according to plan and getting ruined along the way.
What Scott wasn't aware of was the fact that Olivia knew that he had feelings for her or had some kind of liking for her and she had actually always known from the very beginning and she just didn't want a situation where by his feelings for her would get worse and would lead to him believing that anything could work out between them.