Is a contract usurious if it stipulates that my wife works at the university for two years after her doctorate for every academic year, or pays a financial penalty that includes the costs of the scholarship plus fifty percent?

There is no objection to accepting the scholarship in exchange for working at the university for the agreed-upon period, or paying money. This is a permissible compensatory contract. The agreement can be considered, in principle, to be for work, and the payment of a penalty would be a punitive clause.