The case of Katie Meyer at Stanford (not an academic integrity issue but a carelessly punitive disciplinary process nonetheless) shows that universities need to temper discipline with humanity and understanding, and to work for positive outcomes for all students.
> honor system has relied on individual accountability, with students pledging both to refrain from academic dishonesty and to report those they witness in violation
The last part is the weakness. As you note, nobody wants to potentially cause great harm to another student, even one who is guilty of cheating.
That being said, a cheating student should certainly not receive credit for the exam, as it is unearned, creates an unfair environment, undermines the assessment accuracy of course grades, and can disadvantage other students in courses with curved or grouped grade distributions. Widespread or prevalent cheating is particularly destructive because it creates bad incentives.
No one disagrees with this. No one wants to encourage cheating. The question is what works and/or are there any harmful effects of current systems