The claimant's case was "that the subject content [of proposed GCSEs curriculum] gave unlawful priority to the teaching of religious views as compared to non-religious views, including those of humanism. The claimant's case is that the state has a duty to ensure that any educational provision it makes for RE treats religious and non-religious views on an equal footing ...".
The problem arose in an assertion by the Secretary of State for Education that the new GCSE content "is consistent with the requirements for the statutory provision of religious education in current legislation".
Schools have a legal obligation to provide religious education. Under the Education Act 2002 the provision must be "balanced and broadly based".
So the finding is that it cannot be balanced if you exclude non-religious views from the equation and only study religious views. If the GCSE was simply an academic subject and religious education continued to be taught alongside it then I think there would not be an issue. The problem is the assertion by the Secretary of State that the study of this GCSE would satisfy the legal requirement for religious education.