A child brought up by hateful, abusive parents won't grow up to be an upright adult. Yukito is far more realistic with serious flaws in his character. He's not, in fact, as bad as he could be.
It's up to Natsuna to decide if she wants to deal with all that. At least now she knows for sure she needs to deal with something if she plans to be a couple with him. It might have been worse to live for years only witnessing subtle hints, not being sure if a real time bomb might go off when she least expected it.