What does the Misfit mean when he says that Jesus has "thrown everything off balance"?
Jesus throws everything off balance by causing the Misfit to question his murderous lifestyle and even, perhaps, to feel twinges of conscience over his chosen path.
The Grandmother and the Misfit have a relatively long conversation about Jesus. The Grandmother, in terror that she is going to be killed, starts crying out "Jesus, Jesus," meaning to say 'Jesus will help you' to the Misfit. She realizes, however, it is coming out sounding like a curse.
The Misfit responds to the Grandmother's words "Jesus, Jesus," by saying that Jesus threw everything off balance. He goes on a little later to add to this idea:
Jesus was the only One that ever raised the dead," The Misfit continued, "and He shouldn't have done it. He shown everything off balance. If He did what He said, then it's nothing for you to do but throw away everything and follow Him, and if He didn't, then it's nothing for you to do but enjoy the few minutes you got left the best way you can by killing somebody or burning down his house or doing some other meanness to him. No pleasure but meanness," he said and his voice had become almost a snarl.
Without Jesus opening up the possibility of an afterlife, there would, to the Misfit's mind, be no debate between whether to do good or evil: the Misfit's path of finding pleasure in cruelty would be the only logical way to go. This would be his only life, and it would only make sense, from his point of view, to make the most of this one opportunity to be mean to people. At the same time, the way he says "No pleasure but meanness" in "almost a snarl" could suggest he is trying to block out alternative, more compassionate thoughts.
We know Jesus weighs on the Misfit because he gets angry, saying that if he had been there to witness the life and death of Jesus, he would know the right way to live. He begins to acknowledge that he realizes his path is wrong, saying that if he could have known Jesus, he wouldn't "be like I am now." He indicates that he knows that Jesus threw everything off balance when he says, at the very end of the story, there's "no real pleasure in life." It could well be that the Grandmother touched his heart when she touched him and told him he was her child—and that this love he felt from her (connected in his mind to Jesus)takes the joy out of his meanness.
The Misfit is saying Jesus "threw" everything off balance, meaning that because Jesus could raise the dead and perform other miracles, he defied common sense and logic. Of course, the Misfit isn't sure if Jesus really did all he is reported to have done. He does say, however, that if Jesus did what he said, "then there's nothing for you to do but thow away everything and follow Him."
The Misfit chooses the other possibility: "if He didn't, then it's nothing for you to do but enjoy the few minutes you got left the best way you can--by killing somebody or burning down his house or doing some other meanness to him." He refuses to believe in Jesus but wishes he "had been there" for he "would of known and ... wouldn't be like [he] is now."