Back in the end of Season 2, when she goes to the House of the Undying to find her dragons, she has a bunch of visions. One is of the throne room in King's Landing, destroyed by fire. She walks up to the Iron Throne, but just as she's about to touch it, she stops and walks away. So I'm guessing that no matter what happens otherwise, she's going to have the opportunity to take the Iron Throne, and change her mind.