Honestly, with the overblown quasi-religious conspiracies that span on an almost international level -- I don't think the story would ever really be able to handle any of it. The topics of this story were way over its head, way too heavy and way too big. Working on a solution for any of them would turn it into a completely different story.
It's cute as it is right now, honestly. 'it also feels like a hard draft for a much bigger story, in which the girl's tale is a small side-story which describes the consequences of the higher-ups' decisions.