Ok, first thing, his relationship with Justica was not so one-sided. In the period between the planning of the Holy Grail Ritual and the effectual starting of the one (read: Justica's sacrifice to become the Greater Grail Core) they have fallen in love with each other, not the one sided admiration/crush of Canon!Zouken.
And they have even consumed the 'material' side of the relationship.
The result of that night was a daughter, who has been hidden by Zouken, under suggestion of Justica, in another clan allied/associated with the Makiris (Zouken has taken care of having one or more eyes on said daughter descendant, and one of his plans to renew the Matou's bloodline was to adopt/offer a patronage to the youngest descendant, but little Hitomi has revelead herself to be a magus, and the plan has been posponed) to avoid her being used as a guinea pig/political pawn by unscrupolous magicians (himself included, because he know himself too well).
Second thing, in the istant of Justica becoming the Greater Grail, she has used that enourmus mass of power to 'transplant' some of her own circuits, some of the 'light' of the Grail, into Zouken's body.
To make sure he will have ALWAYS remembered her.
Here, Zouken has never forgotten WHY he want the Grail War to be a success.
His soul is not rotten, at least compared to his canon counterpart's.