The faces of both Michael McConville and his older sister Helen are haunting because they are haunted. They are in middle age now. He is 53 and she is 57, and yet to see them interviewed about the 1972 abduction and murder of their mother Jean is to glimpse the children they were. Etched on Michael's face is the fear he must have felt as an 11-year-old boy when he witnessed an IRA gang, most wearing masks, barge into their home in the Divis flats in west Belfast and take away their mother. The masked men had to pull the woman from the arms of her 10 children, who were "crying and squealing". As McConville told the BBC, the fear has not left him; it's what prevents him naming his mother's killers now, even though he is convinced he knows who they are.

You only have to hear that story to know that it cries out for justice. Who can gaze at the eyes of Helen McKendry – who, unlike her brother, is now willing to name names – and not agree with her when she says, "Everybody has that right to know what happened to the person they loved. They need the truth and they need justice"? Who can argue with the advocate of the McConville family and other who have also suffered, victims' commissioner Kathryn Stone, when she says, "There can be no sustainable peace in Northern Ireland until every victim has true peace of mind"? These are surely matters of basic morality, ethical common sense.

And yet, when war and peace intrude, suddenly even the clearest, most transparent moral truth becomes murky. So it is in Northern Ireland, where the leader of the republican movement, Gerry Adams, has spent consecutive nights in a police cell, being questioned about what Helen McKendry believes was his role in ordering the disappearance of her mother.

The drama of this is hard to exaggerate. Adams leads the party that jointly governs Northern Ireland. He was one of the key brokers of the accord that ended what had been a bloody and vicious 30 year war. Yet now he is detained as part of a murder inquiry, asked to account for what part he played (if any) in one of the most notorious crimes of that conflict.

Our first moral intuition surely says that's fine: no one should be above the law. Some make practical objections to such delayed prosecutions, reinforced by specific objections to the Adams case. They note that the evidence is, inevitably, unreliable because it is 42 years old. The testimony of former IRA volunteers, given in taped interviews to a Boston academic project, might not be admissible given that Adams' accusers are now dead and cannot be cross-examined. Moreover, as political enemies of the Sinn Féin leader, those accusers had an obvious motive to attack him.

The people deploying such arguments are making excuses, avoiding the real reason they tremble at the thought of Adams in the dock. The heart of the matter is much harder to say out loud. If confronted with one of the McConville children few would dare say it to their face.

It is this. In places torn by war, there is all too often a choice to be made between justice and peace. We may want both; we may cry out for both. But the bleak truth is, we cannot have both.

Though we have been wary of admitting it, Northern Ireland has been a classic case. One price of the Good Friday agreement was the early release of men of violence who had committed heinous crimes. Justice demanded they stayed behind bars. Peace demanded they be set free. Peace won.

The McConville case poses that tension between justice and peace in even starker terms. Elemental justice suggests there has to be a reckoning for that crime, even if that reckoning goes all the way to the top. But peace makes different demands. As Peter Hain, the former Northern Ireland secretary, put it to me, "Adams and [Martin McGuinness] have been indispensable in moving Northern Ireland from the evil and horror of the past to the relative tranquillity and stability of today."

To pursue Adams now for whatever role he played in that past horror is to jeopardise the current tranquillity. Those far away have become complacent about Northern Ireland, forgetful of the bloody havoc the Troubles wrought, taking today's peace for granted. But those close to it believe it is not irreversible. There is no guarantee that republicans will calmly accept seeing their leader in a cell, while, say, British soldiers who killed civilians in Derry or Ballymurphy walk free. Just because a war ended does not mean it cannot start again.

None of this logic is unique to Northern Ireland. In 1998, the year of the Good Friday agreement, Augusto Pinochet was arrested in London. Chileans who had suffered under the dictator relished the prospect of justice at last. But it never came. In some ways, it never could. The price of the transition to democracy in that country was Pinochet's immunity.

Spain similarly put off its reckoning with the civil war of the 1930s, the country's leaders complying with the infamous "pact of silence" and a 1977 amnesty law, which ensured there was not a single prosecution related to that murderous conflict – but which also made possible the relative calm of post-Franco Spain.

Perhaps Kathryn Stone would look at those places and say the people there have been denied true peace of mind. But they at least have peace. If she wants to see the alternative, she could look at the conflict that once looked as if it might be resolved at the same time as Northern Ireland's: the battle at of Israelis and Palestinians. Both sides in that war know that if peace is ever to come, full justice will be the price.Characteristically, perhaps, we have tried to avoid being too explicit about this moral compromise when it comes to Northern Ireland. We've fudged it, failing to agree any mechanism for confronting the past that might oblige us to admit we are making a sacrifice of justice. Perhaps the Adams case will now force that admission.

But we should remember that Helen McKendry made two demands: for justice, yes, but also for truth. If the former is impossible, there is no reason why the latter should forever be out of reach. It's telling that South Africa's solution was a Truth and Reconciliation Commission – with no mention of justice, a tacit admission that truth might be the most the victims could hope for and, through the truth, eventual reconciliation.

It's time for Northern Ireland to make a similar move, to agree a process that is underpinned by law, that allows for a reckoning with the past, that exhumes the long-repressed truth but which accepts that those who committed even the most dreadful crimes might never face just punishment. Nothing is more painful – nothing, that is, except a return to war.

Twitter: @Freedland