The article is a little unclear regarding whether the University is actually seeking reimbursement of the $415,951.49. First, the article says that the state is seeking this amount from McOwen. Later, the article says that McOwen's lawyer, Joyner, says "it doesn't matter whether he comes up with the money."
My understanding is that, in a computer crime, the total monetary damages are used to determine the severity of the sentence imposed (see http://www.grayarea.com/agsteal.html). I suspect the state is using the (seemingly) large estimate of damages in order to justify a more severe sentence.