After thinking on it a bit it seems like the most likely explanation is a mix of the offence being mild, Japanese corpo autism being Japanese corpo autism and good PR to avoid black company accusations that plague Cover's competitors. I know it is probably wasn't possible because of the aforementioned autism, but if everything is so amicable it's kind of stupid that they didn't just get her to sign a resignation and an NDA before going ahead with a fake graduation. Questionable ethically? Maybe, but in my opinion the obvious best move they had available.
You can criticise the logic of entering a contract regarding secrets with someone who just violated one, but there could always be harsh breach penalties to give Cover some peace of mind. And to continue the game theory, what would they stand to lose from this decision? It gets revealed that Cover allowed the Banpire to save face and fall on her sword? Isn't Japan all about that shit anyway? So based on the information we have I think they made a good move but not the best move they could have. B+ Cover, but that could easily fall to a failing grade if it comes out that what was leaked was so minor that it should have been forgiven.