The Southern Baptist Convention's Ethics and Religious Liberty Commission has warned of a sweeping government attack on traditional Christian views of sexuality and gender – and incidentally highlighted the clash between deeply-held principles and the profound personal needs of those affected by them.

In an article entitled 'The sexual revolution and public education', ERLC director of policy studies Andrew T Walker urges Christians to "take stock of the cultural moment" and inform themselves about what their children are being taught in schools, to establish a "tipping point" or line in the sand about what they will permit and to use their votes to resist government encroachment.

Walker refers to a ruling by the US Court of Appeals for the Fourth Circuit that a transgender boy – a biological female – had suffered discrimination because his school had only allowed him to use a single-occupancy lavatory instead of giving him access to the boys' facilities. The court said that 'GG', the boy in question, could sue the school.

According to Walker: "The impact of the Fourth Circuit ruling is subtle, but sweeping. Government, by circumventing the democratic process, is adopting the approach that the distinguishing hallmark of men and women is psychological self-description."

Walker argues that the court has rejected "biological categories of gender" altogether in favour of a person's own desires: "Apparently, the autonomous, radicalizing self of expressive-individualism has greater authority than chromosomes."

He says: "While I am hesitant to be hyperbolic, I see nothing in the court's logic that would prohibit a boy from gaining access to a girls' shower facility due to nothing but the boy's outward identification regardless of his true desire."

So, he says: "Through non-legal means, and by way of the court system, the government is implementing a systematic top-down push to mainstream transgender ideology by circumventing democracy."

Walker describes the government's action as "secular orthodoxy that puts Christians in a minority". "The idea that human nature is plastic, pliable and subject to re-definition-at-will is a direct assault on the common good and the norms that make human flourishing possible," he says. "Christians must declare, with both compassion and respect, that re-making ourselves in our own image is the very undoing of humanity, for the disavowal of creational limits results in its own form of judgment and human misery."

He concludes: "Though it defies history, reality and common sense, it appears that America is readying itself for a day when all forms of sexual differentiation will be considered discriminatory." He urges parents to "take sober-minded steps to prepare themselves and their children".

However, there is another side to the story. After 'GG' had attended his school for a few weeks and used the boys' facilities without incident, a member of the education board, Carla Hook, proposed limiting restroom use to students' biological genders – female, in GG's case – and providing separate private facilities to transgender students.

At the meeting at which this was discussed, according to the court records: "Many of the speakers displayed hostility to GG, including by referring pointedly to him as a 'young lady'." Others said allowing him to use the boys' facilities would violate their privacy and would lead to sexual assaults; one suggested non-transgender boys would come to school in dresses in order to gain access to the girls' restrooms.

The vote was postponed until the following month. At that meeting some speakers threatened to vote board members out of office if they voted against the proposals. Again, GG was referred to as a 'girl' or 'young lady'. One speaker called him a "freak" and compared him to a person who thinks he is a dog and wants to urinate on fire hydrants.

The court accepted that GG was suffering "daily psychological harm" because of his treatment and had even contracted urinary infections because of his reluctance to use the girls' or private facilities. The "balance of hardships" weighs heavily toward him, the court said.

Whether Walker is correct in his analysis of the situation is moot. What's not in doubt, however, is that as well as abstract theological and legal arguments (the court judgment runs to nearly 70 pages), in cases like this – and in North Carolina, among other places – there are real human stories that also need to be heard. And if an analysis like the ERLC's is being used to back up the opinions of those who think transgender people are "freaks", it ought to be very worrying.

Follow Mark Woods on Twitter: @RevMarkWoods