Seems unfair, but who's to say that if he had contacted them and explained himself, they wouldn't have re-accepted him? Unfortunately, there are so many students who apply to medical school, a school doesn't have to go through the trouble of clearing up a mistake with one applicant; there are plenty of qualified applicants who don't have problems on their applications that they can just take one of them instead.
Oh, and I don't buy the claim that the poor applicant was completely blameless in this. If you get a ticket, they give you a lot of information and it is your responsibility to determine what, exactly, you are being charged with (civil infraction, criminal act, etc.) and how to deal with it. Maybe the student didn't know it was a crime and not a civil infraction, but that is his own fault and responsibility. It is very unfortunate and a shame for him, but if the misdemeanor is from a ticket he was given, he had the knowledge of the infraction and the opportunity to deal with it.