Mrs. Ruttenbai Jinnah
Jinnah's wife's family (Ruttie) were strong Indian nationalists. They along with Ruttie were from the Parsi community who strongly opposed the idea of partition of India. Jinnah's wife Ruttie passed away long before the partition.Maybe because of that Jinnah's only daughter was against her father. Though Jinnah married a Parsi and converted her to Islam, he was upset when Dinah his daughter married a Parsi businessman Mr. Wadia.
There have been numerous other instances where one family member was loyal to India and the other to Pakistan. Allama Iqbal's family were Kashmiri Brahmins and were converted to Islam. Some of his cousins (name Sapru) were not converted and stayed back in India.
Liaquat Ali Khan's wife was not a Muslim. Her grandfather a Hindu Brahmin (Pants)converted to Christianity. When Rennee Pant married Khan she had to become a Muslim and was loyal to Pakistan while her brothers and other family members stayed back in India.
Aziz Munshi, Mr. Chunrigar's family (belonging to Hindu Gujarati high caste) is still in India.
Jinnah himself was from a family who were converted Hindus. Zulfiquar Ali Bhutto's mother was a Hindu who was converted to Islam. Benzair Hindu relatives from her paternal grandmother's side are still in India (Jamnagar).
There is a small Goan Christian community in Karachi originally from Goa, India who stayed back in Karachi (Roland D'souza). Most of their relatives are in India. So is the Parsi community.
------this is from the BBC interview with Nusli Wadia and other sources familiar with happenings in Indo-Pak affairs!.
