I don't think it's correct to say that the statute of limitations has "clearly expired." The alleged fraud included among other things having invoices his company owed submitted to GT for payment. The dispute was about whether the statute of limitations ran from when he put in the orders or submitted the invoices, or when GT later paid them.

I also don't think it's fair to presume bad faith on the part of the prosecutor. Outside the loosey-goosey world of incubators and academia, having your employer pay off invoices for your side business (or personal expenses) is classic white collar fraud.