The first and most important thing to consider in this question of the balance between democratic gains and demands for justice is the most basic function of the state: to provide order and protect citizens while improving their lives. Insofar as that is true, any demands for justice must be considered within the framework of their reconcilability with the basic functions of the state. That is to say, demands for justice can only be considered to the extent that they still allow for the state to provide order and improve the lives of citizens.
This is true for a number of reasons among which being that even notions of what constitutes justice are subjective. To conduct policy and to potentially destabilize and change the face of government on the basis of subjective notions of justice is absurd. Practical challenges to this approach abound, whose notion of justice would we use? How would we ascertain individuals’ notions of justice? Whose notions do we privilege and use as the basis for policy?
Another considerable challenge lies in the reality that in many of these fledgling democracies, many of the perpetrators of violence and atrocities occupy certain positions in the government. Even the acts of violence themselves were carried out not by isolated rogue actors but by the state military and police apparatus. To prosecute and “deliver justice” to all of those complicit in these acts would be to eviscerate the military and police and thus, the state itself.
With all of this said, the symbolic importance of trials against the perpetrators of these acts cannot be overstated. If a country is to move on from these past traumas, at the very least, the appearance of an attempt to pursue justice should be undertaken. To that end, selectively punishing only those most visibly responsible for these atrocities is a good middle-ground.
I completely agree with your argument, and I think your question about whose notion of justice to use is especially interesting. In the case of a newly formed democracy, the answer seems to be the people’s. If the people were to mobilize and demand justice for their current government’s actions, the result could read like a political litmus test. If the government is responsive to the people’s wants, then the democracy would prove its legitimacy and its strength.