^We know from the filmed version of Caspian that the Witch still exists in some form, and further that she has followers who possess the ability to return her to life. It was only Edmund shattering the ice that stopped them, remember. And it's a common conceit of fantasy stories that villains are defeated once by the heroes, survive in some form, rebuild their power, and come back stronger than ever for a final conflict. (Harry Potter and The Lord of the Rings come immediately to mind.)
The big problem with The Last Battle, as Owain noted, is that it feels a bit unfocused; the book starts off with the Ape and Donkey impersonating the return of Aslan, suckering in a lot of rubes, and then takes a sharp left into anti-Arab sentiment with the primary enemy being an evil God we've never heard of before. If I were in charge of the franchise, I'd scrap all of that and replace the antagonists with a cult dedicated to the White Witch, who've succeeded in bringing her back. I feel they could introduce a lot more menace that way, and it would have the cache of building on the established mythology. Anyhow, if the Aslan represents God/Jesus and the Witch the Devil (as indicated by her claim on Edmund's soul in Lion and her temptation of Digory with the apple in The Magician's Nephew), it's thematically appropriate for her to be present at the end of the world. In the Bible, God already defeated Lucifer once by casting him out of heaven (Narnia*), but he's still going to come back for seconds at Armageddon. And you wouldn't write a Christian story series where Satan bites the big one in the first installment, you know?
*(Yea, I know heaven is Aslan's Country, but work with me.)