A loving couple have just lost a Court of Appeal battle to have a civil partnership. What could possibly be the problem? Civil partnerships have been around for years and provide all the legal protections without the marriage label.

The problem in this case is that the couple is heterosexual, not same-sex. Rebecca Steinfeld and Charles Keidan don't want to get married, but they do want to be formally and legally linked. As it stands, the law only allows gay people to be civilly partnered and they want to change that.

The fact that they lost their appeal might have some conservatives breathing a sigh of relief, thinking the judiciary has had a welcome outbreak of sanity. Why not just get married, if they want to be together? But it's not as simple as that: the judges all agreed the law does discriminate against them, they just thought the government ought to have a little more time to sort it out. Among the options are extending civil partnerships to heterosexual couples, or even – according to the QC for the secretary of state for education, Dan Squires, abolishing them entirely.

There's no doubt that the present system is, well, odd, and civil partnership looks very much like marriage by a different name. But for various reasons, some people balk at the m-word. Perhaps most wouldn't bother with a civil partnership, but long-term cohabiters, loving and committed, who may have raised children together, won't get married.

There are all sorts of reasons for this. For some, the word comes with too much baggage. It's an oppressive tool of the patriarchy, perhaps, or it reminds them painfully of their parents' divorce. Some object even to the minimalist wording of the civil marriage ceremony, which only require the parties to say, 'I call upon these persons, here present, to witness that I do take thee to be my lawful wedded wife/husband.' There are no such 'contracting words' in a civil partnership ceremony. And in many social and cultural contexts a marriage is a big deal, requiring a party, expensive and awkward if you aren't a party person.

There are all sorts of questions about it, too. Shouldn't society require people to make some sort of promise to each other if they want the benefits of marriage, however defined? Shouldn't we be able to make a value judgment about it? Why should the state accept that people are atomised individuals, making choices which don't reflect their setting in a whole society? We're all in this together, after all, though the forces of individualism and the worship of the great god Choice are challenging that.

There are particular challenges – and opportunities – for Christians, too. If heterosexual couples are allowed to enter into civil partnerships, what will their status be if they come to church? They clearly aren't just shacked up together for convenient sex, but they aren't exactly married either. So do we approve, or disapprove, or semi-approve? It's all very awkward.

But it's always awkward when our preconceptions are knocked sideways. Because what this legal conundrum shows us very clearly is that Christians have been leaning on the state's definition of marriage for far too long. We've become obsessed by a word whose meaning and status is administered by Parliament, rather than asking what a really Christian approach to marriage might be. In part, of course, this is because we have a state Church that is deeply implicated in what Parliament decides.

For a very long time Church and state more or less agreed about what marriage was. Given the way marriage systematically disadvantaged women until quite recently, that is rather shameful for the Church. Now they do not. So now is a good time for the Church to do some soul-searching about just how far it wants to be tied to the state's definition of it, and how it can make a declaration of spiritual independence.

One way it can do so is by cutting the link between the civil and the religious elements of the marriage service altogether. We could move to a continental system, where in many countries marriage is always civil and a religious ceremony is optional. Ministers would no longer act as functionaries of the state; they would be ministers of the gospel.

In this understanding, the state is entirely free to define marriage however it wants. The Church is entirely free to define marriage however it wants, too. There'd be a considerable overlap, but there's no reason why they should be identical.

And rather than sterile campaigns for 'biblical' marriage which are really campaigns against gay marriage, Christians could stop teach about love, fidelity and forgiveness; about kindness, patience and stamina; about the rich blessings of a relationship between two people whose roots entwine over the decades, who might decide when they're young that they will grow old together and who walk hand in hand with God all the way.

Follow Mark Woods on Twitter: @RevMarkWoods