Phoenix gives a good summary.
Civil cases are between people, who if they wish can proceed with religious civil court.
Criminal cases are between the state and the accused; in a democracy, it has to be separate from any religion because the state in a democracy (India is one), also has no religion (separation of church and state).
I think no religious group should have its own court system, civil or criminal in a democratic society.
Where I live, in Ontario, Canada the government took away all religious civil courts after concerns that women's rights werent being upheld i.e. in family law cases.
They brought everything back into the public civil courts to make sure everyone's rights were upheld.