It is questionable whether Chachamaru has a soul, but that's a philosophical and theological question that is probably inappropriate for these boards. But we know she can love.
Back to the issue here, Takahata poses some good questions but I would like to point out the obvious which he may have overlooked: why isn't Negi with his mother? Even if Negi's mother has gone into hiding, it does not sufficiently answer the question of why she is not with Negi. Unless she herself brings danger to Negi.
A possible theory is that Nagi disappeared because of Negi's mother. Perhaps Negi's mother is some character of importance whom Negi rescued. He might have been sent a new mission after rescuing Asuna, and thus leaving Asuna behind in the care of Gatou and Takamichi. He fell in love with whomever he rescued and had a child. The danger from which Nagi rescued Negi's mother from persisted and they left their child in the care of Nagi's relative so as to give him a good childhood. To date, Nagi and Negi's mother may still be under the same threat from which Nagi resuced Negi's mother from.
The difference between the above theory and others is that the above theory makes the assumption that Negi's mother has yet to make an appearance.