I don't mind court storming, but have always worried about the safety aspect of it. Hundreds of people running down stairs is a recipe for someone getting trampled in the madness. I never really thought about a situation like what happened at KSU this year. I just remember back when Wisconsin had the situation at a football game where a railing gave way and several dozen people fell and were being crushed - I don't remember whether anyone was seriously injured, but it showed the dangers.
Add in what happened at KSU this year and I think you have a very dangerous situation for everyone involved - both students and opposing players or coaches. And honestly, there is not enough security to protect against it. What can a few dozen security do if 500 fans are storming their way?
The penalties ensure that the crowd will do more to police themselves because losing the home game means that there is a possibility that KSU has to play twice in Lawrence in a given year? That's a huge loss for them since they are solid at home, but pretty soft on the road.