I think the reasoning in the books is that if the Dark One ceases to exist, evil ceases to exist, which means humans no longer get to choose to do good. They do good because they don't have any other choice. And Rand realizes that's no way to live. Freedom lies in the ability to choose to do good, even if it's hard. Take away that choice, and nobody's free. Rands realizes this at the end and that's why he decides not to end all evil.