I still think the Queen laid emergency eggs, she knew her Hive was gone and needed insurance to secure the survival of her species. If this was canonized, Alien 3 becomes the Queen's revenge, that Ripley defeated her, but then is impregnated with a Queen. Then the bond in Ressurection becomes a nice change, for three movies its been the Queen and Ripley:
Queen is the Enemy
Queen is the Baby
Queen is part of Ripley 8's Blood and Nature
What a development, to go from sworn enemies to being One!