I mean the alternative would to use her as a womb to produce a suitable matou heir. Which I doubt a lucid and peak Zouken would risk letting her interact with people if that was her only purpose.
Well, I presume that Tokiomi and even Rin would have noticed Sakura going missing suddenly, plus Japan does presumably have some sort of child services and compulsory education. But, yes, you're basically right.
What he did was honestly the nicest think Zouken would do in that situation that was IC for him.
Again, that is not exactly a high standard....
No worms, no grail fragment, no brainwashing into an almost mindless puppet to serve as a baby maker for her whole life.
Yes, it's better than canon, it's just still pretty shitty on his part. Which makes sense for Zouken, yes, but "slightly less bad than worm-raping young children and gloating about it to your descendant" is still not a particularly glowing reference....
He was fucking merciful considering his other options. And he lived up to his bargain with Tokiomi, both his children became heirs to a magus family and lived up to their full potential (at least till Sakura more or less shanked Rin at school during the war).
Well, again, given how dumb Tokiomi is, living up to the bargain they made is not exactly an example of brilliance.
And, ouch, he really did fuck with Sakura, didn't he...?