We need the non-criminal prints because we can then use them to compare against the criminal prints on file with the RCMP when retrieving a criminal record from Ottawa. Otherwise if we were processing a pardon for say, John Smith, there is a pretty good chance we would come up with a criminal record, whether or not it happens to be the correct John Smith or the correct criminal record.
When we retrieve a criminal record using fingerprints we eliminate the name confusion, because even though there are many John Smiths in Canada, each John Smith definitely has his own fingerprint pattern. So for that reason (and because the government agencies want it to be done this way) we must obtain a fresh, new set of non-criminal fingerprints. Otherwise a pardon or waiver cannot be granted.