The first issue is planes are all separate, and each plane has it's own beliefs, systems, and in many cases actual godly figures and gods. So while Gaia, spelled as Gaea within magic cards such as Gaea's Cradle, does exist within the planes of blind eternities, she exists tied to the plane of Dominaria and doesn't actually exist on Ravnica. The closest thing to it as far as a spirit of the plane itself is Soul of Ravnica.
As for the idea of what a godess like Gaea would represent, there would be no conflict there with the Golgari - Gaea represents the natural world, including the cycle of life and death, something which is actually pretty core to the Golgari.
This is based mostly on my own understanding of this though, as again, Gaea does not exist as far as Ravnica is concerned.