I’ve always struggled with this question, not because I see a contradiction, but precisely because I don’t and I have trouble seeing why other people struggle with it. The only real answer I’ve come to is that our concepts of what God is are vastly different. In the same way that some people think that creation was a single event and see arguments of evolution as contradicting the nature of God, I think people who see God as perfect and all loving also see the existence of suffering as a contradiction in the same way. Both are views of God as unchanging being threatened by processes of change.
If, for the sake of argument, we assume that God exists, then we draw about him, simply by the nature of the universe, that he works through process. That creation, and all parts of it, are changing is not a condemnation of God as imperfect, it is only a change in our own perspective of God. For example, recall a place you visited often as a child but then didn’t see again for many years. When you do, your first thought is that everything is smaller than you remember it, not that it has remained unchanged and you’ve grown. In this same way, we change through evolution, science, philosophy, culture, and so our understanding of God changes directly as a consequence. So so that we see him as different through our own process, it doesn’t really say anything either way about whether God remains unchanging or not, only that we perceive that he does.
So what does this have to do with suffering? One of our greatest limitations in this perspective is that we experience creation temporally, whereas creation isn’t simply all space but all time as well. Evaluating the current state in time is only a single slice is like judging a film from a single frame. In that frame we might see apparent compositional errors as relavent to that frame, but in the context of it’s scene and the film as a whole, those sorts of errors may, in fact, be necessary to creating a larger arcing effect to the impact of the film. And this is how we see suffering, we only see it in the momentary context.
Or consider in a more relevant context, evolution. We may see a species go extinct and see it as somehow cruel, but it is merely a consequence of how evolution works, and that the best adapted will survive. Where evolution operates on the genetic level, our choices of how we treat eachother, how we spend our lives, is the direct cause of all of our suffering. And over time, as we experience and witness the suffering, it is our cause to choose to behave in more moral ways. In that way, to say that free will is at fault is as much to blame genetic mutation for creating a maladapted species; free will is our process of change to pursue the goal of relieving suffering.
And, in that same way, suffering itself isn’t even a bad thing any more than pain is bad. Though pain is certainly unpleasant, to call it bad is to ignore that it informs us of injuries and provides incentive against acting recklessly. For those few unfortunate enough to not be able to feel pain, it actually poses serious threats to their health constantly. Suffering is much like pain if all of mankind, or perhaps on a larger scope of all life, could experience it on such a high level. And so, it is only part of that pursuit of that process.
And so, we can see that, over time, it is part of our process of growing and learning. And, unknowing where the endpoint is, we cannot say for certain, but we can certainly say that over a long enough timeline, we will only get more and more toward that state. And so to judge all of creation in that context, suffering is not only an integral part, but it’s part of what makes the whole good.