As I read the article:
1) If there was reasonable doubt that he had committed the crime, his punishment was reasonable due to the presence of reasonable doubt. If it could be proved that he did commit the crime, then the court should not have made the plea bargain, as rape is (to my mind, at least) a very serious crime and not one that should regarded as a potential waste of court time. I suspect that the judicial system disagrees in this regard, particularly in the South.
2) A rape charge does not constitute sufficient grounds for removal from the team. That said, the fact that he was convicted in some sense does indicate to me that there was sufficient grounds for removal. It is, however, still the school's choice.
3) I do not think that removing her from the cheerleading squad in response to her refusal to shout his name is reasonable. It is, however, still the decision of the administrators.
4) Urging her to keep a low profile and in all other ways avoid attracting attention to the fact that she felt she had grounds to press rape charges and that the court agreed with her enough to convict him along those lines, however, is completely ridiculous and totally unacceptable.
5) The ruling is...well, reasonable. Ish. I agree that the fact that it wasn't disrupting any classroom activities makes the school's argument considerably less valid.
I consider this primarily a fault with the judicial system for not being arsed to convict him in the first place, honestly. Secondary failure is the school's, third is the judicial system again.