That's certainly a possibility. Another possibility is that the hatred just rubbed off on Chuck and not God. Chuck was twisted and was somehow able to wrest control of God's powers for himself.

Or perhaps in the beginning God and the Darkness were separate, but in the Season 11 finale when we see them flying off and swirling together, perhaps they mixed into what was almost a single being for the first time before deciding they had had enough and separated before Season 14, and that mixing allowed them to affect each other in a way they weren't able to in the beginning when they were separate. Under this line of thought, perhaps they were able to mix and separate because both agreed on the mixing and separating willingly. But when they merged in Season 15, Chuck wasn't willing to let Amara separate from him again.