I understood his motivation more or less. He's like many other parental/granparental figures in movies who thinks he knows what's best for this kid more than the person raising the child. He doesn't want to snatch out Kubo's eyes in order to harm Kubo, but more as a symbolic way of making him blind to humanity and increasing his magical powers so he can live without all the strife (and beauty) of being human. I feel like that's actually somewhat well-worn territory.
Interestingly, as for his resolution, I wonder if I'd like to watch it again to try to clear that up for myself.