According to the news report linked to by Reason, "The school responded in a letter saying it followed proper procedures and protocols." I know it's probably lawyerese at this stage, but that seems to be the standard excuse whenever a school or the TSA or law enforcement officials do something truly heinous: we "followed proper procedures and protocols."
First, a competitive market for legal institutions would likely recognize that when "proper procedures and protocols" result in a patently absurd outcome, they're probably not very good "proper procedures and protocols." Presumably, there would be enough room for a reasonable interpreter to recognize that this isn't something that needs a "sexual misconduct" classification. That school administrators "are not required to have a parent present for the meeting [in which the confession is signed] unless a student specifically asks for his or her parent to be there" is chilling.
Second, this kind of thing erodes the foundations of legitimate law. If law emerges as a way of solving problems and resolving conflicts, then perhaps it deserves a bit of deference (albeit with thorough review). If law (or "proper procedures and protocols") have simply emerged from the minds of zealous officials and lawyers, then a lot more skepticism is warranted.
In any case of alleged wrongdoing, not merely the defendant but the law itself should be on trial. In a situation like this, I think it's clear that unthinking application of "procedures and protocols"--which are certainly not "proper"--led to a mistake.