DemoSquid was right about the choice.
You can choose to either protect her colony from the Protoss trying to wipe out the Zerg infection or you can choose to eradicate it yourself and destroy the colony.
If you eradicate the colony you are shown the Infested cinematic. If you choose to protect it, you get the Good Man cinematic.
Also I was correct in saying that it wasn't Kerrigan talking to Raynor though Infested Hanson. When she says "my children" she means her colonists.