I think you're missing that the very fact that you had to wonder if you were running afoul of the honor code is what makes people compliant. The Harvey Mudd honor code specifies "integrity" - but what does this mean? When there aren't clear definitions, people start to imitate others, especially those who are assumed to know what the rules really are. The punishment for violations doesn't even need to be explicit, the threat of being ostracized or losing face is a strong enough disincentive for many people. The fact that you internalized the values of the community means you perceived them as just, so for you, the self-policed rules were legitimate. And maybe they were legitimate. But here's a big problem: the administration is not operating transparently, they are counting on social behavior to control students according to a hidden set of rules that aren't up for discussion or debate, unlike an explicit rule book that could be questioned and contested.

The problem with the disciplinary board follows the same logic: just as vague, open-ended rules create more compliant behavior, you should expect that a student-run disciplinary board will also penalize deviant behavior much more enthusiastic precisely because the administration is hands-off.

The important question is whether the (explicit or implicit) rules are good rules, not whether you're permitted to self-police them. Self-policing may be more efficient, but the cost is less transparency and more conservative behavior.