I think there are two answers to this question, one of which is stated directly in the book and the other which is hinted at. Firstly, Kira's world and in particular her village is set in a dystopian future, after a massive, cataclysmic event, the Ruin, destroyed the earth that we know. It is clear that the poverty and dangerous conditions in which Kira's people live are part of the response to this, as we see a remnant of humanity trying desperately to hack itself out a life in the wilderness and being returned to almost stone-age levels of development.
However, at the same time, I think that as the novel goes on there are hints that the Council of Guardians actually use their power to control and manipulate and keep certain groups of people in their poor and desperate state. It is highly interesting that before Kira is selected to work for the Guardians, every carrot and tuber is precious to her as she struggles to survive. When she begins to work, she has plenty of food and enjoys luxurious living conditions. There is definitely a disparity of wealth in this society, as is made painfully clear when Kira and Thomas visit the Fens:
On the other side of the stream, beyond the thick poisonous oleander bushes that were such a danger to tykes, lay the area known as the Fen. In some ways it was similar to the place that Kira had called home: the small cotts, close together; the incessant wailing of infants; the stench of smoky fires, rotting food, and unwashed humans. But it was darker here, with the trees thick overhead, and festering with dampness and an odour of ill health.
Comparing the two realities--that of Kira and Thomas with their wealth and those that live in the Fens--seems to indicate that this new society is just as bad as creating the haves and the have nots as we have been.
Kira's village might live in misfortune and ruin because the village's decisions are all decided by the Guardians, so their lives are literally being controlled by a group of people. The Guardians may be forcing groups of people into poverty and despair on purpose.