There seems to be a certain moral ambiguity about this act that you yourself have highlighted. On the one hand, killing is never a "good" idea, but as you point out, the contextual considerations could lead us to agree with Eva when she says that she killed her son out of love. Morrison paints a terrible picture of what life was like in Bottom, ironically named, and we are forced to ask ourselves hard questions about the extent of love and how love is defined in such situations.

In the novel, Eva attempts to justify her actions when her daughter Hannah questions her about the killing.  Eva claims that killing Plum was the only way to set him free.  She argues that because Plum was so dependent on her, he had no life or options for himself.  Hannah does not think that Eva loved them as children; however, Eva says that the sacrifices that she has had to make over the years prove that she loves her children.  So if "justify" means to have a clear reason for acting in a particular way, then Eva's actions were "justified" according to what she reveals to Hannah.  Maybe one could argue that killing her son was not the best decision, but this would depend on one's moral values.