There is no way that John should be accused of being a witch, or of being guilty of practicing witchcraft. It is implied that the people accusing him use the following reasons to support their accusations: 1. He hasn't been to church in quite a while. 2. He hasn't had his last son baptized. 3. He is openly antagonistic and questioning of the town's reverend, Parris. 4. He committed an affair with Abigail. 5. He "coerced" Mary to come and testify against the girls and the courts, supposedly to try to get real witches set free.
The first three accusations he explains in act two when Hale comes to visit. He hasn't been to church in a while because his wife was sick a lot the past year, and, he doesn't like Reverend Parris or his preaching style. The fact that he doesn't like Reverend Parris also accounts for his arguing with Parris a lot, and not wanting his son to be baptized by him. He gives good reasons for not liking Parris--Parris seems fixated with money, wealth and status, and preaches scary sermons filled with Hellfire and damnation. So, people use this to say he is against God, and a devil's servant, which is ridiculous.
He openly confessed to his affair, at his own detriment, but the courts didn't believe it, so that wasn't taken into account when he was accused of being a witch. It was Mary Warren turning on him, in order to save her own skin, that led to his arrest. She lied, told everyone that he had forced her there to lie, and that he was "the devil's man." She did this so that Abby and the others wouldn't accuse her of being a witch. And, the courts take that as proof, rock solid. For that reason alone, he should not be condemned as a witch.
At the most, John is guilty of making a few mistakes, and being a bit prideful and expressing his opinions. Not witchcraft. There is no proof he ever cast a spell, bewitched anyone, or used the devil's power to manipulate. I hope that helped a bit; good luck!