You highly underestimate what it means to have a such a tight knit family. They might not like what he did but enough to commit patricide? They don't have the guts nor are they fucking moronic enough to throw their organization in chaos by doing such a thing.
Furthermore, Murasaki would no longer be compliant at all if they murdered her father. Before she was remaining obedient to protect Shinkurou but if they up and killed her father who had finally approved of her will and actions she would probably just up and kill herself, leaving the Kuhouins with absolutely nothing.
The end was excellent, it obviously couldn't be a "Shinkurou and the loli live happily ever" kind of ending given the scope and strength of what he was fighting against. That would be truly nonsensical.