Clara is as much a product of her own upbringing and prejudices as anyone. In Kill the Moon her faith in her own perceptions is shaken and she must accept that things are not always as they appear. Its not only her view of the moon that changed, however, but also how she sees the Doctor. As her hero worship fades she starts to realize the Doctor is a more complicated and ambiguous figure than she initially realized. This both angers and terrifies her. The premise of this episode is complete nonsense though to be fair some of that may have more to do with production decisions than what was written in the script. Theres nothing wrong with an absurdist approach but without any logical thought behind the visual choices the story begins to falls apart. Why were creatures likened to bacteria portrayed as spiders? Why would they spin webs when there was no prey to catch? Why did a being that lives in space look like a dragon? It might make more sense if the creatures portrayed werent so literal.