This is, of course, a matter of opinion. My own view is that John is not disrespectful in “By the Waters of Babylon” because he does not truly defy his father’s advice or the law. His father repeats the law to him, but clearly accepts the idea that John is going to break the law. While John does break the letter of the law, he seems to accept the spirit of the law, and he breaks it because he feels that it is, in a sense, his duty to do so.
Early in the story, John does seem to disobey his father’s advice. He goes to his father and asks his blessing for the journey that he (John) is about to undertake. His father tells him
It is forbidden to travel east. It is forbidden to cross the river. It is forbidden to go to the Place of the Gods. All these things are forbidden.
John acknowledges what his father says and agrees with him, but he says that it was only his father's voice that spoke, not his spirit. In other words, he did not really mean it when he agreed with his father. It seems clear from the story that John’s father understood this and accepted it. He tells John,
Once I had young dreams. If your dreams do not eat you up, you may be a great priest. If they eat you, you are still my son. Now go on your journey.
From this, it seems clear that John’s father tacitly accepts what John is going to do. If his father accepts what he is going to do, John is not really defying his father’s advice.
Similarly, John is not really disobeying the law. He constantly looks for omens that tell him whether the gods accept what he is doing. When he sees these omens, he continues. Before he crosses the river, he worries about whether he is doing the right thing. He cries as he makes his raft, knowing the law forbids what he is about to do. In other words, he clearly respects the law, but he feels the gods are, in a sense, telling him he has to go. He believes he cannot be a good priest if he does not break the law. He says
If I went to the Place of the Gods, I would surely die, but, if I did not go, I could never be at peace with my spirit again. It is better to lose one's life than one's spirit, if one is a priest and the son of a priest.
In other words, John feels the gods have told his spirit that he has to go to the Place of the Gods. He is technically breaking the law, but he is doing so because he feels it is his duty as a priest. Therefore, in my view, he is not really defying the law.
In these ways, I do not think John is being disrespectful. He really cares about his father’s advice and the laws. He feels that he is called to disobey them, though. He does disobey but, in my view, he does so respectfully.