If everything originally posted is true, I wouldn't worry too much about the unpaid portion, since I'm sure he will receive back pay. The problem is management using strong arm tactics to try and force people flying into a situation they are not comfortable with. Kudos to this guy for standing up and doing the right thing, even if it does mean going through this hassle.
I don't think I'll ever understand management's side of things. At our airline we are required to use the autopilot on approaches in IMC, yet it can still be MEL'd. So anytime you want to practice handflying an approach in IMC we are technically violating our company policy...that is until the autopilot is MEL'd.