Actually sounds reasonable to me. You should be able to get a refund on the excess withheld tax ...in about a year (that's what sucks).
The real question you need to ask your tax person: If you refund the bonus pro rata, does that mean the bonus was "unpaid" to you and therefore you don't owe tax, and are therefore entitled to a refund on excess withheld taxes?
It's possible the bonus is considered income which cannot be "unpaid", in which case you might owe full tax on the $10K at whatever your usual bracket is. The fact that you pay the company some money to relieve your contractual obligation to them may not undue the original transaction. Better ask a real expert.