Good All Along: Alfred wanted to turn his daughter into a doll (aka kill her) to prevent her from suffering the same madness he does. He even mentioned that he wanted to kill her while "she is still pure". He could see that madness beginning to show when she starts to kill animals.Seeing that Monika isn't 100% sane either regarding her nightmare fetish, it might be justified, even if she doesn't turn out mad.
Based on their very similar appearances (long black hair, fringe cut straight across, same blue eyes), and the fact that we know a teenage/young woman version of Aya does exist in Ogre's world (if you see the True Ending). Miss Library will worriedly comment on her father, who spends all of his time cooped up in his laboratory - then point out she's the same with books, ending on the line "It runs in the family, I guess." This is the last line of Mad Father, uttered by Maria. Plus, as of Misao 3.0, if you try and name Miss Library "Maria", she will comment that she doesn't like that name, but will take it anyway (note that the version of Aya created in Ogre's world doesn't have the real Aya's memories of surviving the ordeal at the mansion, growing up with and eventually running a doll-making clinic in the woods with Maria, and therefore would still dislike her).
- The Steam version of Misao will have Miss Library refuse to be called Aya, as "only Father can call [her] that name..."
Both are really similar in appearence and Dio is known for creating an army of zombie as his minion. Given his big ego, it is possible that Dio is narcisstic enough to create a little zombie version of himself which is probably doubles as a backup plan to keep his presence around should he die.
Mad father has a Dio expy as one of the allies while Misao has some sort of Yoshikage Kira's expy as the main antagonist, it is only logical for the third game to have an element of Diavolo and Doppio (or even a straight up expy of them) in the antagonist and the protagonist. The split personality element will give an unpredictable atmosphere to the story and probably gives an interesting plot twist of both the protagonist and antagonist being the same person.(aside from the Cat Demon) known as the Crow Demon. The Crow Demon specialized in medical and pharmecudical equipment and experimentation, and often granted Ellen painkillers to deal with her illness. Ellen didn't deal with this Demon for actually curing the sickness, because that's what she contracted the Cat Demon for and thus he had to grant it his own way.
When we get to Mad Father, we see Ogre as the one letting Monika have her vengeance on the household. Not only that, but there's quite a few things in game that seem to deal with him. For one, Ogre is the one responsible for giving Dr. Drevis the tools and knowledge he needed to make his dolls. The Doctor is a doctor for a reason, and got that medical knowledge from Ogre. Finally, the save points in game are Crows, which mimic how the Cat served as the save point because he was really a demon. The fact that Ogre is helping Aya could imply that he is the Crow demon too given the Cat Demon is a Justified Save Point. Which brings us forwards to Misao.
In Misao, Ogre reappears as Onigawara, and here he's responsible for letting Misao have her vengeance on the student body of the school. He also conveniently serves as the only save point in the school, which if he is the Crow Demon, also fits in with the Crows being the Save points in Mad Father. Even more evidence of his connections to medical knowledge is that game is known for having quite a few callbacks to Mad Father. The main ones being Mrs. Library and the Laboratory section in the game, with a mad doctor wielding a chainsaw looking quite similar to Dr. Drevis. In the 2017 rerelease, he even has his private quarters that house dolls of all kinds, and Mrs. Library even rejects being called Aya as "Only father can call [her] by that name. As can be seen in some endings to Mad Father, Onigawara is responsible for setting the doctor back up there and continuing his work.
In short, Ogre/Onigawara is the Crow Demon as described in the Diary of Ellen, and the evidence from the various games.