Yes, he was expecting her to have powers. That is clear from the warnings about bleeding from the eyes, and her hiding that from him. The father he arranged to 'adopt' his daughter also knew that it was a possibility and that it would still be ok. The neighbor even tried to convince his terrified family still to take her.

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The problem is how powerful and violating the astral-projection/mind-control are. We, the viewers, just don't know how prevalent powers are or how often they can be almost completely benign (ability to talk to squirrels). Invisibility/temporal field/flying+shockwaves+strength are the other powers shown and they are counterable (we see each of them defeated) and don't violate a person's autonomy. Her powers are just beyond what everyone was expecting.