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Margaret helps Sook out more than once—first in Sydney, when he's falsely accused of murdering her husband, and then later, in Hokitika, when he's hiding in anticipation of killing Frank Carver. However, she ultimately sells him out by telling George where to find him, which results in Sook's death.
When explaining why Margaret was so generally inclined to help Sook out, Shepard tells Devlin that she was "fond" of him. Shepard was totally disgusted by the extent of her loyalty:
She lied. Under oath. She defiled her late husband's memory—my brother's memory—by calling him a suicide…and all to protect that worthless chink from the punishment. (III.10.39)
Of course, in the novel's present-day narrative, Margaret had a reputation of being almost pathologically meek and submissive to her husband and generally fearful—and from the fact that she ultimately turns Sook in, we can probably assume that Shepard had bullied her into changing her alliances and repenting her past kindness to Sook. Which actually says a lot more about Shepard than it does about her, come to think about it.