From the Data Stand point from the TKA01 Table. So if Business Area and Company Code combinely assigned to the Controlling Area in TKA02 Table. What if the Business areas are deleted from the Company Codes then even Company Codes will be deleted along with the Business Area or else if only business areas are deleted from Company codes having multiple Business areas then there are duplicate records with same company code and Controlling area assignment which is not allowed. How is this situation handled.
I suggest you reread Christian Ortner's correct advice above. Business area is not assigned to company code, so there is no way this scenario can occur. It is most definitely not best practice to delete company codes anyway (the preferred solution in my experience has been to shut them down and leave them, deactivated, in situ).