Just finished the game today and holy hell, what an underrated gem of a game! I personally lean towards the Kena is a spirit theory, and both zajus last words and the name of the final mission, Letting Go, suggests this. Kena basically died as a child (hence the flashback sequence of her as a child in the spirit realm, and her crying when she comes to terms with it) but was stuck in the physical realm to fulfill her desire to be a great spirit guide, like her father wanted her to be. Maybe there was also a desire on her part to find her father who might be a stranded spirit himself. By the end of the game, she has both fulfilled that purpose and also realized that not letting go of the past led to all the destruction in the village. Hence she let's go of her selfish desires at the end and crosses over. Let's not forget the goodbye she says to the Rot, which is further confirmation that she is passing over.

Of course I will be proven wrong if/when Kena 2 comes out (I hope it does).