Hi man,
The thing is that the credit memo with reference is precisely affect the balance of the Customer - Sales Area, imagine a Report by Sales Area saying the total Sales Amount of the Sales Area is 1 million, but then you turn to another sales area and discover that the same customers have credit notes for 1.5 million, insane. The purpose of referencing the credit/debit memos is that, not to lose track, including Sales Areas. Otherwise make no sense to create it with reference, just create a Credit Memo with the customer you want to affect in the sales area you want to affect, no reference. For audit purposes justify the document based on REASON FIELDS and approvals, let me explain this a little more:
One single person CANNOT create Credit Memos, cos this could lead to wrong ethical behavior, to avoid this some companies recommend to have more than one person involved in the process of Credit notes creation, what I've done on this situation is: provide access to one person to CREATE Credit/Debit memos using the standard transaction VA01, in the settings of the Sales Order Type I customize that the document will be created automatically blocked for billing (can use a UserExt to always have this field populated on the creation). This person WONT have access to modify Credit/Debit notes (VA02) but his supervisor will and this supervisor is responsible to approve and modify the blocking field to release the doc for billing. Yes, he can also change the amount but you will already have the log of changes in place for audit purposes.
This is more than a technical issue, a process issue. My kind suggestion is to challenge the business and get clearly why they want to have a referenced Credit Memo without using the Sales Area of the based Billing Doc.
Hope it helps...
Saludos!
Ricardo