I think that Hanna's illiteracy can be seen as a metaphor for moral illiteracy in a couple of ways. The first is that Hanna never really takes any action to remedy her illiteracy when she is young. She continues to hide, evade, and deny that there is a problem. This obstinance towards taking corrective action is a metaphor for a sense of moral illiteracy. She does not take any action towards the role she plays in the camp or concern herself with what is going to happen with the prisoners. The moral illiteracy she experiences is similar to her lexical illiteracy. In both settings, illiteracy is a metaphor for the inability to take action.
Another way in which illiteracy is a metaphor for moral illiteracy would be in Hanna's restoration which takes place when she is in jail. Hanna takes corrective action from the lowest of levels and provides some sense of redemption given her own condition. This is a metaphor for moral illiteracy in that Hanna learns the error of her ways and what transgressions she has committed. In this setting, the need to overcome illiteracy acquires a sense of moral restoration. The need to take action and the initial resistance towards it are examples where Hanna's illiteracy can be seen as a metaphor in the novel.