When Jesus stood before Pilate, and Pilate had the authority to save Jesus’ life or to condemn Him to an excruciating death, Jesus told him “You would have no authority over me at all unless it had been given you from above.” How would that have sounded to Pilate? I think that Pilate probably took it to mean “You won’t harm me; God won’t let you.” But we know the end of the story already, and so we don’t read it that way. We read it more as “Pilate, it’s not up to you, it’s up to God…” And of course, we know that God chose to cause His Son great suffering in order that we could be saved from our sins in a just manner. But let’s consider a similar dialogue in the context of a story where we don’t know the ending from the beginning… Imagine a man standing in front of his boss at work, and his boss is saying “If you refuse to falsify this information, I will fire you!” And the employee replies, “You know, as a Christian I believe in always doing what’s right. Your threat means nothing to me because God is in control of all things.” Now surely the boss will take this to mean “You couldn’t fire me if you wanted to!” But I imagine that this story could more than likely end in the employee being fired. So when we meditate on the fact that God is in control of all things, it gives us comfort that no matter what happens, everything is going to be alright. But hopefully most of us are mature enough in our faith to realize that this means everything will be alright, even if we get fired from our job! (Or whatever other misfortune it may be.) Some people would look at the outcome and say that "God clearly didn't come through for you... maybe He doesn't exist!" But surely we can see that maybe from God's perspective the best move is for this guy to get a new job with an honest boss!
God is in control of all things, which means nothing happens that isn’t according to His will. And it is apparent that His will is to allow suffering, and to allow sin. I don’t think you can deny this. But that doesn’t mean that God can’t have preferences. When we are faced with several options in life, it’s not the case that only one of them is “God’s will” and all the others aren’t. It’s not the case that only one course of action is “righteous” and all the others are “evil”. Sometimes you can choose between two courses of action, both of which are good. Do you give some amount of money to charity or do you spend it on your wife? Every particular case is different. There may be some cases of this where God might approve of either course of action equally, whilst at other times He would say “to spend it on your wife is ok, but to give it to charity is better”, and then other times it may be that case that to spend it on one rather than the other is actually a sin! To give a real example, consider how the Pharisees thought themselves terribly righteous in donating to the temple, when Jesus said (and I paraphrase) “Actually, you’re robbing your parents of the support you should be giving them in their old age!” So even from God’s perspective, morality isn’t black and white without “better and best”, “worse and worst”. God can will there to be sin and suffering whilst still having a preference for there to be neither. In other words, God can will two different things (that there be sin and suffering, and that there be no sin or suffering), and have a preference for one over the other.
In the case of God, who cannot do any unrighteousness, both of these “wills” must be righteous, and maybe that’s where we will really struggle here. But I think that to allow sin and suffering in the world doesn’t make God unrighteous. For example, sometimes the pain we experience in suffering is necessary in order for God to be righteous! If we don’t somehow punish our children when they’ve done wrong, for example, we ourselves are actually unrighteous in failing to correct that behaviour. Or we've seen that it might be righteous of God for us to lose our job rather than be subjected to ongoing temptations or perhaps persecution in that workplace. God can also have a righteous reason to allow sin. One possibility is that sin demonstrates God to be true because we are never better off when we’re in sin. Whenever we are able to compare our lives with sin and without sin, we will always say that it’s better without, and thereby we prove that God is right in prescribing the conduct for our lives which He has prescribed. Unfortunately, many people aren’t prepared to take that leap of faith to discover what life might be like without sin. But those who have found Christ and have overcome sin can all testify that life is better without sin… (even when we lose our jobs because we refuse to sin.) When I personally find myself miserable or depressed for no apparent reason, I will often come to realize that I've been letting my behaviour slip in some way.
We know that God’s preference is for there to be no sin and no suffering because these are things He will ultimately do away with. They are devices He presently uses (wilfully) in order to demonstrate to us His power and His love. His power and love are demonstrated when we discover that through Him we overcome both of these things. Through Him we overcome suffering in that even while we suffer we have peace and faith and hope. And through Him we overcome sin as He empowers us to turn away from it. People who oppose the existence of God on the basis that a loving God would not allow sin and suffering I think fail to see how God’s love is expressed as a result of the existence of sin and suffering in the world. How would we know the extent of God’s love if He had not comforted us in our darkest hour? How would we know the extent of God’s love if He had not forgiven us despite the most wicked things we had done? And while I don’t expect that this closes the case on the problem of evil and the perplexity of God’s sovereignty, I find it is sufficient to at least be able to say and believe, without being intellectually dishonest with myself, that there can be an all powerful God who loves me and who also allows me to suffer and to sin.
I am the vine; you are the branches. Whoever abides in me and I in him, he it is that bears much fruit, for apart from me you can do nothing. (John 15:5)