I like the idea of both needing the other. Especially since nothing in this show points to the conflict between Cylons and humans being resolved in a military way - there won't a grand battle in the end at which the Cylons are defeated, or a master virus from which they all die, etc. And they won't just go away and stop finding the humans, either.

Moreover: Kobol is referred to by the Cylons and the humans as the "beginning of us all", where "gods and men lived in harmony". Their version of Eden. In one of the deleted scenes, we get the fellowing fascinating information:

Tigh: Why did we leave Kobol? I've forgotten.
Elosha: One of the Gods wanted to be more important than the others. And thus the war between the Gods began, and men left Kobol.
Six (who is listening with Baltar): Blasphemy. There has always been only one God.

If this ends up as canon in season 2 (i.e. if there is an onscreen scene using the same idea), you have a story of mankind leaving Eden not because of something they did, but because of something the beings they worshipped did. And the solution to that conflict might have be union, the acceptance of both visions as complimentary, not contradictory. Note that so far the Cylons aren't the only ones who show exclusive tendencies and "we're right, you're wrong" interpretations; both Starbuck and Helo get very upset when a Cylon talks to them and invokes religion, claiming that this is just for humans.