When the family was starting yes, but then they started to inbreed and even the Imperator told them to stop being that way, but even so they refused to change.
So no, they would never allow Tsubaki to be with someone outside the Yayoi family, and you already explained the problem with the kisaragis.
Maybe but Hakumen specifically said that because of her he was not another casualty in the war, i don't think that has anything to do with guilt.
Other thing we need to have in mind, is that most of the scenes in the Drama CD happen just a couple of days before Jin went after Ragna (and we know the effect Ragna has in Jin:v:), and they tell us just a little about their interaction when they were together in those six months before that.
Then the scene between Tsubaki and Hakumen in the story mode is very revealing, Hakumen asking her to let him see her face and phrases like "Unfortunately our situation changed", "I was foolish", "...I lost her"
That didn't struck me as if he was talking out of guilt when i first watched it. I think maybe Jin was aware of Tsubaki's feelings, maybe not or maybe he realised his feelings for her once she died.
And about Jin and the moon, yeah i never understood that, why does he hate the moon? and what did he mean with "another moon is falling"? so if anyone know please post it.
