The ship has probably sailed at this point, but does it say you have to pay back the bonus if they fire you? If not, then potentially you could have just refused to work the excess hours. (They could fire you ... but you wouldn't be leaving.)

And you said that the contract says "$20k minus applicable taxes". That sounds exactly like you need to pay back only what you received. What is their explanation for why they are saying otherwise? Show HR the language of the contract and say "no".