Well technically a Guardian is no longer 'alive' thanks to the traveler. So Bungie can kinda get away with it, however I hate how if you play an Awoken they don't mention it once that they're of such breed. I'm a way you're playing a Dark Souls-esk story, as a 'chosen undead' but in space.

I was an Exo on my first play through, and I figured she was calling me "it" because I was a robot. I thought, that's a nice, subtle touch, well played Bungie. Then I played it again as an Awoken and realized her speech pattern was just an excuse to not have to record the dialogue twice (once for he and once for she). Needless to say, I was very disappointed.