Owen is certainly one of the strangest heroes in any text that I have ever come across. His diminutive stature combined with his high pitched voice make him an incredibly memorable character and it is difficult to avoid liking him, in spite of your best intentions at times. John forgives Owen because of who Owen is and what larger ideas Owen represents to John. Even when they were young, it is Owen's ideas and beliefs about God and fate that help shape John into the man he is today, and this is made clear in the opening paragraph of the book:
What faith I have I owe to Owen Meany, a boy I grew up with. It is Owen who made me a believer.
Owen, therefore, through his friendship with John, won his forgiveness. Remember too that Owen gave John his baseball card selection as a token of forgiveness. It is the massive impact of Owen on John's life that causes John to forgive Owen for the accident that led to his mother's death.