Before the exodus of New Caprica, everyone besides Roslin, Big Adama, Doc Cottle and Tory, thought Athena’s child died.
Judging by Cavil’s actions since the knowledge of Hera’s exisitance made known, he is a lot less inclined to just kill all humans now that Hera exists. Maybe just the fact that he doesn’t want to kill Hera in the process.
Now that resurrection hub has been destroyed, Cavil went to great length to bring Hera back. Perhaps just for study, but it shows how important Hera is to the Cylon race.
In that case, if Roslin didn’t swap Hera for a dead baby, had Athena been on New Caprica with her baby andt he rest of the human population, would the Cylons treat humans differently on New Caprica?
Further more, even if the Cylons were enlightened into the spirit of true cooperation with the human in light of Hera, would it still end in failure, due to violence brought on by excessive anti-cylon sentiment?