According to Chuck co-creator Chris Fedak, Sarah's memory is slowly returning and Chuck and Sarah will fall in love together again; it will just take time.
From an interview with Chuck co-creator Chris Fedak:
Alan Sepinwall: I want to start at the end. They sit on the beach, Chuck tells Sarah the story of their relationship, she laughs, and we've gotten hints that she's starting to remember her life with him. And he kisses her. Does Morgan's magic trick idea work and she remembers everything instantly? Or is it just going to be a slow and steady process for her to get all her memories and feelings back?
Chris Fedak: I think I'm going to leave that up to the audience. I have my thought, and Josh has his. It's a sweet, nice moment. A happy ending for those two. I think it's up for everyone to judge that kiss at the very end.
Alan Sepinwall: Well, after last week's episode, a few commenters were upset with the idea that Sarah's memory had been erased, and that all her character growth we had spent the last five seasons was for naught. What would you say to that?
Chris Fedak: I would certainly say it's not erased. It's not all gone. It hasn't been five seasons all for naught. It's in there. And the fun will be remembering it and falling in love again. How could you imagine anything better?
Later in the interview:
Alan Sepinwall: We find out what most of the other characters are going to do, and Chuck and Sarah are on the beach, so we know they're going to get back together. But what do you see as the rest of Chuck Bartowski's life being?
Chris Fedak: Wow! Well, that's a gigantic question. I will tell you this: I see Chuck and Sarah together, being a husband and wife, starting up that computer security firm. Hopefully they won't find themselves dodging bullets for the rest of their lives. Of course, as a writer, now I start thinking, "You know what? They could get into a little bit of trouble." That gets the story side of my brain going. But for now, they're happy and they're together and thinking about their future.
In his series finale review, Alan Sepinwall gives his impression of what happens to Chuck and Sarah based on his interview with Chris Fedak:
When the amnesia storyline kicked in last week, some of you expressed concern that five seasons of character growth for Sarah were being thrown out the window. I don't think that's what happened (nor does Fedak, as you can see in our interview). Whether or not Chuck's kiss performs the Disney princess trick and breaks the evil spell all at once or not, it's clear Sarah is coming back. She remembers how to stock the Wienerlicious counter. She remembers Irene Demova. She remembers them carving their names into the frame of their dream house. And as Chuck tells her the story of their great romance, you can see her slowly beginning to connect with the rest. If she's not all the way back now, she will be eventually. He's her Chuck, she's his Sarah, and they get to fall in love all over again, and that's pretty damn sweet. We may not know exactly what the future holds for those two (Fedak also talks about that a bit), but we know that they'll be together, and all the rest is details. Once upon a time, Sarah was Chuck's guide into a strange new world, and now he gets to return the favor.