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."