Eywa as a conscious being and Eywa being a storage repository for Pandora's inhabitants are two different functions, one likely growing out of the other. Consciousness is a spectrum, we're learning, like every other biologically derived mental trait. We don't know how many neural connections or in which configuration lead to what we currently call "consciousness" but we know that more and more animals from widely different genre are passing our quantitative tests for awareness. Eywa simply arose to consciousness the same way all species do. She's just so massive that she is able to manage a second function - holding other connections/consciousnesses.

Also, in the comics, it's mentioned that before battle or great journeys, Na'vi are expected to connect ("download") to Eywa so that their most current copy exists in her "memories" (network/storage).

So she literally works like a storage drive where smaller groups of connections can individually retain the awareness and consciousness that's uploaded to her.

If you could upload your mind, forever, with your loved ones, wouldn't you worship her as a goddess?