QUESTION: “In John 1:3 it says that through him all things were made; without him nothing was made that has been made. Does this mean that God also created sin?”
ANSWER: You're not alone in being troubled by the question of where sin and evil came from. Theologians have even coined a term for the age-old debate – "theodicy". Part of that study addresses your question: If God is holy and just, and, as you say, cannot even look upon sin, and if He is the only true God who created all things, then how did evil, temptation, and sin ever enter His good creation?
I'll start by saying that there is a great mystery here. We can't (in this life, at least) know a full and satisfactory answer to this question, because God has not revealed the answer. His Word simply doesn't address it directly. But there are a few things that we do know about the origin of evil and sin based upon Scripture.
First, we know that sin existed before the fall of Adam and Eve. God created the angels, and they were all "very good". However, somehow they were tempted and some of them chose to sin by rebelling against God, resulting in their being cast out of heaven. Therefore sin originated with Satan and the demons (fallen angels), not with the rebellion of Adam and Eve. Satan tempted Eve to sin, God didn't. But the Bible tells us very little about that original rebellion among the angels, and nothing about how the angels were tempted to rebel or how it was possible.
When John says in the verse that you quote, "All things were made through Him...", he is referring to the creation, the material world. Sin isn't a "thing" in the same sense that trees, animals, stars, and human beings are created "things". Sin is an action, a choice, an attitude, a desire. God created Adam to be "very good", and by giving Adam an opportunity to choose to obey or disobey, God allowed for the possibility of sin entering His creation. But He didn't tempt Adam to sin or in any way cause him to sin. The desire to rebel came from within Adam, and it wasn't placed there by God.
We can know that for us, as fallen human beings, temptation and sin aren't things that God created, because James clearly tells us, "Let no one say when he is tempted, 'I am being tempted by God,' for God cannot be tempted with evil, and He himself tempts no one. But each person is tempted when he is lured and enticed by his own desire. Then desire when it has conceived gives birth to sin, and sin when it is fully grown brings forth death." (James 1:13). Since the fall of Adam and Eve, the real origin of sin is in our hearts.
While the Bible teaches that God doesn't cause us to sin or tempt us to sin, it does teach that He is sovereign over our sins. In a mysterious way, He is able to incorporate our sinful choices into His great plan for the world, and particularly for our redemption. Joseph said to his abusive brothers, "As for you, you meant evil against me, but God meant it for good, to bring it about that many people should be kept alive, as they are today." (Genesis 50:20). Peter showed this relationship between God's sovereignty and our sins in the way he spoke about the events of the cross: "...this Jesus, delivered up according to the definite plan and foreknowledge of God, you crucified and killed by the hands of lawless men." (Acts 2:23). Somehow God incorporated the sinful choices and actions of the Jewish leaders into His sovereign plan to send His Son to the cross to die for our sins. We don’t know how it works, but it is comforting to know that God is in total control of the sinful activities going on around us.
That also means that God not only knew about the sins of Adam and Eve, but He also incorporated them into His plan for the history of the world and for our redemption even before He began to create the world. Ephesians 1:4 says that "He chose us in [Christ] before the foundation of the world, that we should be holy and blameless before Him." Again, there are mysteries here that we are not able to understand, probably both because the truth is really beyond our puny comprehension, and because God has not chosen to reveal the answers in His Word.