Not having gone into the code but having played upto date.
I would say yes atleast from my play through killing him is not avoidable.
But the Dev would need to confirm it.
It looks like you are meant to kill the dad.
(and if i'm honest I agree however I hope it's shouldn't be detrimental to the MC's path).
Again I'm guessing but I suspect by doing so you release Mary's sister.
From the situation she possibly was trapped in through no choice of her own.
And that would then possibly lead on to mary and her being reunited?.
After all it sounded like Mary believed the hold daddy had on her Sister.
Would prevent her sister from leaving of her own accord as Mary had.
And on top of that lets face it if anyone in the game deserved it he did.
Just my opinion mind you.