At the very beginning of this excellent novel we are told that Kira's mother died after a "brief and unexpected illness," which does little to raise our curiosity until we begin to understand more and more about the society in which Kira lives and the way that the Guardians in particular have absolute power and control. When we meet Jo and Thomas and realise that they are orphans too, our curiosity is somewhat heightened, but obviously, both for us and Kira, what really makes us suspicious of what has happened to Kira's mother is when her father, the "giftie," according to Matt, is brought to Kira, and Kira hears the truth of what happened to him and how Jamieson disposed of his rival. Knowing that the Guardians are capable of such acts makes it an easy link to suspect them of having killed her mother. Note her thought patterns as she deduces this:

Her mother's death: a sudden violent, isolated illness. Such things were rare. Usually illness struck the village and maney were taken.
Perhaps her mother had been poisoned?

Therefore, normally illness was not "isolated." Many would be affected and die. This leads Kira towards the unescapable fact that her mother was cruelly killed so that the Guardians could gain control over Kira and her talent, and therefore shape the future as they want.