I always thought the Cyth represented "God" and "religion", imposing order on humans so they could control them and feed off their fears etc etc. Then the Goddess was Mother Nature, representing anarchy and chaos and our base animal instinct which was being enslaved by religion and rules and civilisation etc. And Slaine was the warrior for that side of things, fighting against the system, order. In this tale though, there is now talk of another "God" - the Trinity - who cast out "Lucifer and his angels" from "heaven"...and Lucifer and these Angels are the Cyth. So the Cyth are the Devil? But the Goddess is someone else. And all these faerie folk that used to live in happiness ended up turning to the dark side because of humans becoming all religious and losing the magic from their lives?
So theres the Cyth and theres Mother Nature and they are at war. The Cyth try to restrain humans with religion and order, Mother Nature tries to free them using Slaine as her tool.