I haven’t read this entire thread, just wanted to weigh in on the subject as it’s a very important one.
God is obviously ultimately responsible for everything that goes on in the cosmos (and in heaven as well) since he created it and has the ability to stop it if he so chooses. Christ even claims he is responsible for everything that happens:
“18 And Jesus came and said to them, “All authority in heaven and on earth has been given to me.” Mt. 28:18 (NRSV)
Now, the question “how could God allow suffering” actually has to deal with whether or not the suffering is justified or not. I will assume the suffering is unjustified. I would also have to disagree with the statement that God is “moral” (if “moral” is defined by how natural man understands morality) because I think it is very clear that the God of the Bible would be considered to be evil by human nature (see the following passage). This brings us to one of the most interesting passages in Scripture:
“9 For three and a half days members of the peoples and tribes and languages and nations will gaze at their dead bodies and refuse to let them be placed in a tomb; 10 and the inhabitants of the earth will gloat over them and celebrate and exchange presents, because these two prophets had been a torment to the inhabitants of the earth.” Rev. 11:9-10 (NRSV)
Notice that the human race is overjoyed when the two witnesses are dead and even celebrates the occasion. This is very important because the two witnesses are basically corporate representations of God, Christ, the Holy Spirit, the Apostle Paul, Peter, Elijah, Moses, etc. This shows us something very important about human nature: human nature believes that God is evil.
That being said, I wanted to answer how God could allow unjustified suffering: God can allow unjustified suffering because God will rectify all unjustified suffering on the day of judgment. All unjustified suffering will one day be made right by God. So God can allow it for a time (to accomplish his purposes, like saving the elect), because he will right it all later and make it as though it had never been. God can do this, man cannot. And so God can allow unjustified suffering.