Pain – the pain experienced by animals and the ineffable pain experienced by those, e.g., swept away in the Indonesian tsunami and those who loved them – is a product of the laws of the physical universe, specifically the Second Law of Thermodynamics, also called the principle of entropy, which observes that all physical being – our bodies, our cars, our homes, our forests, the entire physical world – is in a continuous process of breaking down and falling apart.
Suffering, the existential consciousness of alienation, on which you are so eloquent, is an extension of human freedom. Those of us, like you, who stand in the faith and view the world (both physical and existential) from the perspective of faith, do not have words to understand why God created the world in the way can has, but we do understand that both the principle of entropy and human free will are gifts of the Creator and that God respects the integrity of Creation.
For millennia God has been placed in the dock before the tribunal of human misery. The person of faith lacks the wherewithal to make the case for God but knows that Godself does not need the benefit of human advocates. The Christian (or at least the Catholic Christian, I cannot speak for others) knows that God is not insensitive to human misery and that God, in becoming incarnate in the person Jesus Christ, walked with us in our misery and drank the cup of human misery down to the dregs, as the model and price of a life of utter integrity.