Possession of authority and the exercise of it are two different things. If popes, bishops and clergy used the authority given them by God to bring about evil that, though sinful, does not invalidate that authority. Remember no one is impeccable, not even the popes and the bishops. If the exercise of authority depended upon being sinless then no one could exercise it so to recognise the bishops' abuse of their authority does not entail moral acceptance of that abuse.
It is very much in vogue these days to make meaningless gestures such as apologising for historic offences. It is naive to suppose that St John Paul II's long list of apologies achieved anything; those who committed the offences are dead as are the perpetrators. Tony Blair apologised for the Slave Trade but as far as I'm concerned he wasn't speaking for me as I wasn't involved no more than I was part of the Inquisition.