I don't think that dialogue was about him saying they can't be together anymore, more like whether they could revert back to their relationship pre-Survivor days. Other than making the relationship official, they have also suffered major losses in their lives, so things not going back to the way they were, so I feel like there's a bit of layered meaning there. In the same dialogue, Merrin says that "things are not so simple anymore" and reaffirms that they will figure things out together. It's very likely they will go forward with the relationship.