I agree with you completely that intent to injure deserves a suspension, permanently on the second offense. The problem is that the rule, as it is currently written, makes no mention of intent. In fact, if you watch the NCAA video, it is very clear that any contact to the head is to be called a major penalty and game misconduct. With all the attention that concussions are getting these days, you can bet that the NCAA is not going to be happy with the current enforcement of the rule and it will change during the season. I watched 2 games Saturday evening and honestly only saw one check where the point of impact was above the neck. It was called a minor for roughing; this was not the intent of the rule. However, the fact that I only saw one hit to the head may mean that players are being more cognizant of head contact.
The NHFS and NFL have both set precedent with their contact to the head rules (NFHS in several sports and NFL obviously in football). The onus has clearly been shifted from the player being hit to the player doing the hitting to make sure there is not head contact. There is the argument that a player cannot stop on a dime, which is true, but the hitter is going to be expected to. Almost every sports medicine and AD meeting in high schools these days has concussions as a point of discussion. Since the summer, we have had almost a dozen high schools sign up with my ambulance service for HS football game coverage (the past NFHS rule required either an ambulance or MD) and some have even extended the ambulance requirement to soccer, lax, and hockey games. The good news ... Army contracted us for the first time to cover their hockey games.
It definitely seems to me that refs are rule as they were instructed to. It may not be fair, but if the force of the hit is to the head or neck, it must be a major penalty, regardless of intent. I think the only place where judgment comes in is if the contact was centered at or below the shoulders but the head was involved. These hits are much less likely to cause concussion syndrome (or worse).