I believe Olivia Dunham showed a bit of jealousy when she found out Peter Bishop was making contact with her sister. So yes they will eventually get together but it will be a very long drawn out process. Don't forget she is still recovering from the man she was in cinta with being a crook and dying. So it will be a while in coming.
I think it's possible; however, Olivia seems to be the type of person who is married to her work. Therefore, I think it's gonna be a while before anything romantic happens between her and Peter.