Did you continue to send in the Illness Benefit forms every week since you returned to work... cos there are two sections to the form one for people who continue to be unable to work due to illness and the other side which is the final certification of incapacity? I dont understand how the department continued to pay you in such an instance given payment is only processed on receipt of completed forms (which is generally weekly or alternatively monthly). If they paid you and you never completed or sent in the illness benefit claim form over that six week period since returning to work - that would obviously strenghten your case in relation to the administrative failures of the system!
Anyhow, doubt very much if they'd be taking you to court - that in itself costs money.... and you as you said you've proposed a repayment schedule. Once you stick to it - you should have no probs.