What to do with transgender people? It's one of those very modern issues that evangelical Christians face with bewilderment. At one level, it's seen as a sign of the times: another manifestation of society that's turned its back on God and is running by different and unChristian rules. At another, it's more than a bit yucky: the idea of the radical surgery chosen by some transgender people is viscerally disturbing.

And of course there's the associated issue of sex, and for evangelicals sexual behaviour tends to define discipleship: should transgender people still do it? If so, with whom?

Some can't cope with these questions at all. I've heard horror stories of transgender people turning up at church and being told to leave and not come back. Others have been the subject of heated church leaders' meetings at which the loudest voices were calling for them to be banned. At least they had the conversation. Others – and perhaps this is a commoner experience – have been politely but hurtfully shunned and marginalised, as a congregation has been unable to own and understand its discomfort and confusion at someone who transgresses one of the most basic human norms.

Tapping at the door, though, is a fundamental gospel perception: that transgender people are, after all, people, made in the image of God. They are not monsters and they are not evil incarnate; they're just folks, and if the church has nothing to say to them, perhaps it has nothing to say to anyone.

All credit to the Evangelical Alliance, then for attempting to provide some guidance to its members. Its new booklet Transformed, by Peter Lynas, aims to open a conversation in an area most churches have probably avoided. It does its best to avoid stigmatising trans people and its approach is, up to a point, compassionate and nuanced. It avoids laying down the law in areas such as 'naming', where for instance hardliners would argue that it's wrong to call a former David 'Deirdre', as it's conniving at falsehood; that's not Lynas' view, he tells me. It's informative on matters medical and legal. It's written for an evangelical constituency whose instinct is probably – alongside that of many in society at large – to reject trans people automatically, and in that light it does something to advance the cause of grace and understanding.

While much of the booklet is factual and impartial, it does begin, however, from the position that to transition is, at some level, wrong – though it's not put in so many words. As such it probably chimes with the views of its constituency, but it can't really claim to be even-handed. The only story it tells is that of 'Tim' and his struggles with the fact that his father transitioned to become 'Stephanie', who is then repeatedly misgendered ('he asked God to take being trans away and when that didn't happen, he decided it must be for him'). This simply reflects Tim's own usage about his father, I was told, but it looks bad; a footnote would have been helpful. And when I interviewed him, Peter Lynas said he had not deliberately talked to transgender Christians before the booklet was produced, though he did talk to groups in Northern Ireland which included some 'people of faith'. A subsequent interview with a woman who's experience gender dysphoria is to be included on the EA website soon. 

Its section on the Bible is interesting, partly because it's rather thin (inevitably – it's not something the Bible discusses) and partly because its interpretations seem rather selective. Discussing the Ethiopian eunuch in Acts 8, for instance, Lynas says correctly that he 'did not fit within a binary understanding of gender', but that he 'encounters God on the way home', stressing that 'the text identifies him as a "he"'. The point, however, surely lies in the eunuch's question: 'Why shouldn't I be baptized?' 'Lots of reasons', is the obvious answer in a booklet of this kind, but Philip baptizes him without question; his gender status is irrelevant. Of course we don't know whether the eunuch chose his status (historically, some have) but the story could have been explored in quite a different way.

There's a sub-section repeating what's often held to be the theological basis for rejecting the idea that someone can legitimately transition. Genesis says God creates male and female; reality is binary. Cross-gender identification 'distorts the creational order of male and female'; it's part of living in a fallen world. The booklet quotes Oliver O'Donovan, who says that 'maleness and femaleness forever defines an important aspect of the relationship Christ has to all of us, His church'.

But while these arguments might work as illustrations supporting the presupposition that it's wrong to be transgender, they're hardly strong in themselves. The church might be the Bride of Christ, but it contains males and females; it's not 'female'. This is a multi-layered analogy that can't possibly be used to refer to transgender people. And surely no one really thinks Genesis 1 is 'about' transgender. It cannot be prescriptive, saying that people 'ought' to be male and female, as the option of changing sex didn't exist when it was written. It's descriptive, just naming people as they generally are.

And we know very well that people are not just born as male and female, but with disabilities of mind and body which we are glad to be able to cure. We don't blame someone for having a heart murmur or spina bifida; we try to heal them, or to enable them to live with their disability in the way that's best for them. It's not a moral issue but a therapeutic one; but for some reason, gender dysphoria is held to be 'different' and maleness or femaleness is privileged above any other identification. And if it is true that in the Bible, 'biological sex is binary and integral to personhood' (how could it not be?) the idea that 'biological sex should reveal and determine gender' [italics mine], as a critique of transgender, is a really startling logical leap.

It is, in biblical terms, rather odd then that transgender should be moralised in this way, and it's hard to escape the conclusion that biblical texts are being made to do things they were simply not designed for.

I suspect that there are two reasons why it's so difficult for many Christians. One is sex – the assumption is that if someone transitions from one gender to another, an opposite-sex relationship they might have would be homosexual rather than heterosexual, which most evangelicals would find unacceptable. But another is that there is a powerful and increasingly mainstream ideology that sees transitioning not just as a legitimate response to genuine gender dysphoria, but as part of the deconstruction of gender altogether. In this light, it's to be resisted in principle, because of the potential for harm that such a sweeping-away of millennia-old norms could do.

Transformed suggests this is about individualism and ideology, emphasising 'chosenness' over 'givenness'. There's undoubtedly truth in this, but it doesn't come near the case of people tormented by real gender dysphoria. It also suggests a parallel with Gnosticism the ancient creed that saw matter and bodies as fallen and inferior; transgender people, it suggests, have an idea of a 'real me' trapped inside the wrong body. 'Any form of Christianity that devalues the body and the physical creation in general is deeply problematic,' it says. Indeed; but I'm not so sure all transgender people devalue the body. People with gender dysphoria are likely to be obsessed by it.

A section on 'cultural trends' – including relativism, feminism, post-structuralism and cultural Marxism – locates the debate over transgender issues in the wider currents of today's thinking, with a huge pull-quote from Isaiah 59:14 ('Justice is turned back, and righteousness stands at a distance; for truth stumbles in the public square, and uprightness cannot enter') driving the point home: it's all bad.

But is it? It's perfectly true that the idea of huge numbers of people being 'trapped in the wrong body' who could be 'cured' by a simple operation and a bit more understanding and acceptance is nonsense. But arguing that there is no such thing as gender dysphoria (and this booklet accepts that there is) or that there is always something 'wrong' about transitioning, even in cases of the most acute mental distress, surely goes too far the other way. Minds and bodies don't always work the way they should; this should not be hard for us to process.

However: once this has been said, there is still much, much more to say. Some trans people would be deeply offended at the idea they were experiencing a form of disability; it's just who they are. And who's to define what's appropriate dress or behaviour for males and females, anyway? Once we try to prescribe things like this, we start to oppress. This is part of a conversation evangelical Christians need to be having, and which has barely begun – though in wider society it is already in full flow.

Some elements of that conversation are deeply alarming. There's a school in Brighton, for instance – Dorothy Stringer High School – where no less than 40 pupils aged between 11 and 16 say they don't identify with their birth gender, while 36 more are 'gender fluid'. This is not, on the face of it, very plausible, and we might reflect that it seems to be fashionable. But what happens when children aren't challenged about this, or are even encouraged? Some 80 per cent of children who attend the Tavistock gender clinic before adolescence change their minds; for those who come during adolescence, 80 per cent follow through. But there's very little research into the effects of transitioning. A recent Channel 4 documentary, Trans Kids: It's Time to Talk featured psychotherapist Stella O'Malley, who struggled with gender as a child and was 'absolutely certain' she would have transitioned if she'd been growing up today. She said of evangelists for transgender today: 'What if they've got this wrong? What if everything I had was what they're feeling, because it certainly sounds very, very, very like it.'

And she said: 'I think they're being led. I think they're lost and I think they're being led.'

She added: 'It's right to ask legitimate questions about people who may regret transitioning, or the lack of research into the drugs to make sure we are not doing harm to kids.'

But even asking these questions can be next to impossible. A Radio 4 Women's Hour series has seen Jane Garvey attempt to conduct a discussion, with mixed success. There is a 'trans doctrine' which is unchallengeable, with campaigners refusing to appear with those who don't subscribe to every particle of it. Another presenter, Jenni Murray, wrote an article in March arguing that women who grow up male don't experience the world in the same way as those who were born female; she was blacklisted by Stonewall and accused of being transphobic. Germaine Greer was pilloried for saying transgender women were 'not women'. The government has recently finish a consultation regarding updating the 2004 Gender Recognition Act; if it ever comes to parliament, it might make Brexit look simple.

And the complexity of the issue – which the EA recognises up to a point – means that Christians ought to be very slow to comment, and very careful in what they say, particularly if they want to have an effect on the conversation happening outside the church; and they absolutely need to hear the voices of transgender people themselves. Taking the line, as Transformed does, that transitioning at whatever level is fundamentally problematic is likely to limit that engagement

The views expressed or assumed here not self-evidently evangelical or biblically orthodox, though they support what are likely to be evangelical presuppositions. There's a better conversation to be had, and it might start with evangelicals sitting down and talking to transgender Christians. Personal experience should not dictate theology, but good theology can't be done without taking account of it.

Mark Woods is the author of Does the Bible really say that? Challenging our assumptions in the light of Scripture (Lion, £8.99). Follow him on Twitter: @RevMarkWoods