I was thinking the girl, easy enough to pretend with the duck down command for the guy

That's a good point about the children thing, I wasn't thinking about that. With the really high detail models though, you could probably get the body proportions right to make it more obvious, and of course it would have to be stated in-game that it is definitely a midget(probably multiple times to be sure, as that'd be a pretty bad confusion to have).

As for the story, I'm not creative enough to think of anything good, but I imagine there could be plenty of interesting scenarios

I don't think that a disclaimer will solve the problem, especially with a character like Tsukuyomi Komoe. I read her character description in the TuaroMajutsuNoIndex-Wiki, and I think the biggest problem is that she physically appears like a 12-year-old, and that she sometimes acts childish doesn't make it any better. Stating that all models are intended to be 18+ won't keep people from saying that this is only a vehicle for paedophilia. They will look at Tsukuyomi, they will see a 12-year-old girl, and that's all, they won't listen any further.

I guess that critics will tear the disclaimer to tatters as a weak attempt to justify the depiction of child pornography. You can't tell people what they are supposed to think of you, they make up their own picture. Hell, the girlfriend of a fellow student was 25 years old, but because of her petite figure she looked like 15, and many people looked at him with disgust when he kissed her.

What I want to say is that you walk on thin ice with this midget thing. Perhaps instead of starting from Tsukuyomi Komoe, you should begin with a curvaceous woman of smaller build... And with pubic hair. Found a picture of Tsukuyomi having sex on Google. No good.