While on the run with Hae-Joo, Sonmi talks with An-Kor Apis of Union twice. The first time, he's disguised as a holographic carp. He tells Sonmi that he hopes "together, we may change corpocratic civilization out of all recognition" (7.1.41). This tells us that Union's goals aren't just to free fabricants but to destroy Unanimity.
From that point on, everything Sonmi sees seems to be an event calculated by Apis to turn her toward their cause. By the time Apis shows her his true face, he says that he wants her to see one more thing before making her decision to join them—as if, by this point, she has any choice. When Hae-Joo shows her the cannibalism taking place in the fabricant Xultation chamber, the deal is sealed. It's hard not to think that Apis manipulated her from the beginning.