Please don't listen to everything that you read on the internet, this can be considered check fraud and I would not suggest it. It probably wouldn't happen but if the school wanted to, they could take legal action and it would end up costing a lot more than $1,000.
There's been a few forums regarding this subject, so I would suggest reading up on it before making a decision:
Stop payment on a deposit check
Have anyone put a STOP on their deposite check?
Friend sent non-refundable deposit to hold seat now wants to stop payment
Also, it sounds like the check has already been cashed and withdrawn from his account so a stop payment wouldn't work anyway.