To me, the fact that the man is not allowed to have his kids shows that there is a lot more to the story than we've been told.
What I get from this story is that Salford Children's Services is stating that the children do not consider themselves Muslim and they have not had a Muslim upbringing while they were living with their mother - as the judge said "In the light of the court’s finding as to the children’s previous upbringing, the local authority has made it clear that it does not propose to treat the children as belonging to the Muslim faith".
The father probably did not have much access to his kids when he was estranged from his wife and since her death has been to court many times to try to get custody - which is often the position fathers are in regardless of religious background if they want access to their children. If the kids genuinely don't consider themselves Muslim because of their upbringing, then the father is just going to push them further away if he keeps trying to convince them to become Muslim every time he sees them - and it will make the kids feel rejected. If he is just telling them about his beliefs and background without pressuring them, he is giving them some sense of their background and heritage, which is fine.
Not sure what to make of the allegations of domestic violence and assault - he has denied it and there has been no prosecution so not sure if they are factored into any decision by the Family Courts.