So know that you will have to pay it all back shouldn't be a surprise if you renege/leave etc.
If that is the case, then they should have been aware of the repercussions. However, the article appears to suggest they left because of the pay clawback - not the other way round. If they really were over paid 'in good faith', even after querying it, they have a right to be miffed.
Army helicopter pilots quit in overpayment row - BBC News