THE debate about Scottish independence is about identity and how we measure the distinctiveness – or otherwise – of Scotland.

It's also about the things which are the staple diet of politics – economics, defence, education, health and more.

Inevitably this debate touches on and involves the life of churches. I believe that churches should be agnostic – indeed should be absolutely determined not to have a view – on issues of constitution, flags and governance. In the membership of our churches there will be people on either side of this debate. They are entitled to hold and to express their views without finding themselves any more or less respected as members of our churches.

There are deeper issues too. Churches believe that faith should colour and enrich the whole of life. So membership of a faith community should connect to deeper questions of identity and belonging in our society. You can see that in the names our churches – the church which I represent is the Scottish Episcopal Church; our national church is the Church of Scotland; and so on. We should feel good about that. Faith should not be privatised, compartmentalised and pietistic.

But of course there is a shadow side. The curse of my native Ireland is sectarianism and we have our share of it in Scotland as well. Sectarianism arises when people's search for identity uses religion as a way of gaining presence and authority. Religion then becomes a marker of division rather than a builder of bridges. It's easy to see that at work in the flag-waving disturbances of Northern Ireland and on the football terraces of Scotland. More subtle but no less serious is the situation which would arise should religion and identity become intermingled in the Scottish independence debate.

There are however two areas in which it is appropriate for churches and faith groups to be involved.

We understand that Scotland is distinctive in its legal system and its attitudes to education. Also significant are the impact of the Scottish Enlightenment and the Scottish Reformation. I find myself exploring with people the values which make Scottish society distinctive – whether we are communitarian rather than individualistic; whether we are diverse and inclusive; the strength of our links with the rest of the world through the Scottish diaspora and many others. People should think about the specialness of their own society and the values which are expressed in it. Whether that specialness and distinctiveness should be expressed in political and constitutional independence is a political debate in which churches and faith groups do not belong.

The second question is one which I approach with some caution. At the recent General Assembly of the Church of Scotland, there was debate about how the relationship between church and state should be expressed if Scotland chooses to become independent. That's a very important question – sometimes expressed by asking whether it is meaningful to say that we live in a Christian society. Through our shared membership of the Anglican Communion, we in the Scottish Episcopal Church are aware of similar pressures on the established-church status of the Church of England.

Those pressures arise from societal changes – Government proposals for same-sex marriage and the failure of the Church of England to end gender-discrimination in the appointment of women bishops. So there are important issues to discuss.

More important is the way in which the national church status of the Church of Scotland gives it a leadership role in the wider faith community as we seek to share faith in a secular society. In geographical terms, the Church of Scotland sees this as the "territoriality" debate – about how the ordinances of religion are to be shared with the whole population of Scotland. The Kirk is clear that to fulfil that challenge will require the support of its partner churches. So the more important discussion for us is not about constitutional issues but about how patterns of shared ministry can be developed across Scotland.

So churches should not come down on one side of the political and constitutional issue. But the independence debate gives us important opportunities to discuss within the faith communities and beyond the nature of the society in which we want to live and the place of faith within it.

The Most Rev David Chillingworth is Bishop of St Andrews, Dunkeld & Dunblane and Primus of the Scottish Episcopal Church.