For the present, I can only draw together a few thoughts.
There is nothing like the ruthlessness of ideologically-driven violence to wake us up from our illusions and remind us that sin is an offense against God.
The trajectory of sin leads to a distortion of reality that aspires to be an inversion of goodness. Sin (which includes even our own seemingly pedestrian sins) radically aims to "make evil to be good" and to "make good evil." Not surprisingly, as sin proliferates, it becomes a driving force, a program of violence, an "organization" designed to inflict cruelty and suffering on the innocent, to deform consciences, to spread destruction, to brutally and ruthlessly attack human beings and eradicate the human heart's desire for transcendence.
In the midst of it all, those who are afflicted wonder, "Where is God?"
We Christians cannot evade the mysterious weight of this question.
We should listen to the compelling stories of those who have endured these awful evils. Some of these stories are very, very hard to bear, and no one should take them up with idle curiosity. We should help one another to engage the facts and personal testimonies regarding the atrocities of the recent era, seek guidance from those who are more experienced and mature in faith, and find ways to participate in the ongoing process of healing.
A war, a persecution, a genocide may be "in the past," but wounds and scars remain. There are people who still need help, materially and spiritually.
Hopefully, what we learn will spur us on to a more serious commitment to love God and love our neighbor in every aspect of our lives. We will also be "shaken up" in a way that might lead us to pray harder, read and meditate more attentively on the Scriptures, recall the teaching of the Church, and turn more ardently to the all-encompassing suffering of the crucified Jesus. And we will be reminded of the need to rededicate ourselves to opposing evil, and seeking to overcome evil with good.
Of course, none of our efforts in this regard will make all of the concreteness of human wickedness and the terrible affliction that results from it "go away."
But they will draw us into a deeper faith and hope in the One who is greater than all our understanding, who calls us to endure with him our own afflictions, to fight against injustice as best as we can in this world, and to suffer with others even when all seems lost and they are utterly broken and powerless.
The question remains: "Where was God in 'the killing fields'?" People experience the pain of this question even today, and it's important for us to feel the force of it in our guts.
This doesn't mean we should lose confidence in God and his love for every human person. But the truth about history will strip this confidence of much that is sentimental and root it more firmly in the actual reality of God's love, beyond our feelings, beyond our understanding. It can awaken in us the courage to follow God's love to the peripheries of this world and hold fast to it in the most desperate extremities of life.
"Often we cannot understand why God refrains from intervening. Yet he does not prevent us from crying out, like Jesus on the Cross: 'My God, my God, why have you forsaken me?' (Mt 27:46).
"We should continue asking this question in prayerful dialogue before his face: 'Lord, holy and true, how long will it be?' (Rev 6:10). It is Saint Augustine who gives us faith's answer to our sufferings: 'Si comprehendis, non est Deus'—'if you understand him, he is not God.'
"Our protest is not meant to challenge God, or to suggest that error, weakness or indifference can be found in him. For the believer, it is impossible to imagine that God is powerless or that 'perhaps he is asleep' (cf. 1 Kg 18:27). Instead, our crying out is, as it was for Jesus on the Cross, the deepest and most radical way of affirming our faith in his sovereign power.
"Even in their bewilderment and failure to understand the world around them, Christians continue to believe in the 'goodness and loving kindness of God' (Tit 3:4). Immersed like everyone else in the dramatic complexity of historical events, they remain unshakably certain that God is our Father and loves us, even when his silence remains incomprehensible."
~Benedict XVI, Deus Caritas Est 38