Hazrat Inayat Khan gives a Sufi explanation of the apparent inconsistencies and injustices in God’s dealing with humanity.

Mankind tends to consider that all that is pleasant has come from the mercy of God, and all that is unpleasant either from the wrath of God or not from God at all, because he thinks that God is just and merciful. In reality God’s goodness and mercy and justice are hidden under all pleasant and unpleasant experiences in life. We call things unjust when we cannot see their justice; things are unpleasant to us when the standard of our pleasure is limited; things appear unmerciful to us when we restrict and limit mercy. But sometimes things that do not seem just to us, are just according to their real nature; unmerciful things often contain a hidden mercy. Therefore the Sufi takes all that comes from God with resignation, seeing and recognizing in it His mercy, goodness, and justice.

We, the children of the earth, are like children, all through our evolution, to our heavenly Father; and in our ignorance our actions are like those of a child. If the parents give it sweets, it takes this as their kindness; if they give the child bitter medicine, it considers it anger on their part, not knowing that in giving that bitter medicine they show their kindness just the same. There are many things that we think are good for us, but in fact they may be the worst possible. One person cannot obtain a certain position which he wanted; another cannot settle in a town where he desired to live; another is unable to visit a city that he wished to see; while sill another does not succeed in gaining the wealth he wished for. All such unpleasant experiences make a man discontented, and if he has not enough faith he begins to think that there is no such being as God. If we only considered how perfect is that mechanism of the infant’s body, and how it works in such an orderly way, we should see and realize that there is a power behind everything, with full wisdom and understanding that sets all things going harmoniously, and it is the same with the mechanism of the whole universe.

There is a story that Moses had sought to associate himself with Khizr, the guiding angel of all seeking souls, and had requested to be allowed to follow his path.* Khizr said, ‘No, Moses, teach the law that is given you; our way is complex.’ After great persistence on the part of Moses, Khizr complied with his request, on one condition: that he should not interfere with his works, by any means, in any way. When on the seashore they saw a little child drowning, caught by a wave, and the mother calling loudly for help, Moses wished to run and help them, and he wanted Khizr to do the same. Khizr said, ‘ I have told you not to interfere with my works.’ Moses said, ‘ Oh, would you allow an innocent child to be drowned like this when you can help? How dreadful!’ Khizr said, ‘Think of your promise and do not say another word.’ They went on farther, and took a boat to some port, and while in the boat Khizr began to enlarge holes that were already in the boat. Moses said ‘Oh how cruel! Anyone who sits in the boat will be drowned!’ Khizr said, ‘It does not matter. Think of your promise, and do not say one word more.’ Because of the great persistence of Moses in asking him to explain what it all meant, Khizr said, ‘ The child that was drowning would have brought many families to destruction, therefore God intended that, before he became able to do so, he should be drowned. We have done nothing but allow the will of God to take its course. And the boat in which I made the holes, on its return will carry thirty robbers who intend to destroy many lives in a certain village in order to accomplish their robbery. It was meant by God that, as they have prepared themselves to destroy innocent lives, they should be destroyed before they can do so. This shows the meaning of a Sufi verse:
‘The Controller of the world knows how to control it,
Whom he should rear and who he should cut off.’

* This story is related in Quran 18:65-82.