Formal rules or code of honour

Probably all business schools ask their students to sign a code honour or conduct during the first days. What you usually agree to is that you will be honest, doing your best efforts for the course and only submit materials for grading which are a result of your "unaided efforts". Bottom line: thou shalt not cheat.
I've seen schools where the code of honour is taken extremely seriously. Perpetrators often identify themselves and submit to their peers' trial and punishment. Conscience and group commitment play an important role here. In such schools, exams are taken without supervision and individual specific situations are dealt with on a case by case basis, assuming that the students have acted according to the code of conduct.
On the other hand, all schools have formal rules, like consequences for deadlines not met. Such rules are important, as they work as a guideline for most standard situations. They make decisions easier.
But what happens when both clash against each other? A formal rule was broken due to an irrelevant mistake, without the any disrespect to the code of honour. The teacher has every right to apply the penalty provided by the formal rule. But, by doing this, wouldn't the teacher signalise that the student's word of honour is worthless and, therefore, relegate the school's code of honour to a mere piece of paper?