How can a European like Picasso appreciate African art without he himself being African? Its simple, recontextualization. Kierkegaard, like the Bible, is not something an atheist attempts to ignore as literature, but something they ignore as a context within which to frame their world. One does not have to belief in Narnia to appreciate the novels. Similarly one does not have to share anything whatsoever with the artwork to be able to appreciate it, it is the magnitude of difference we often appreciate.

Let me ask you a similar, inversed question. How can theists reconcile their tribal beliefs with scientific inquiry? The answer is all to similar. A Christian, for example, has to extend the biblical metaphor that "God Created the Earth in 7 days" to be symbolic of a larger time frame just to accommodate the findings of evolution. I mean, we have a decent enough understanding of biology to disprove all metaphysical concepts of the soul, so now the soul is ephemeral.