How to return multiple values for THEN clause in an SQL CASE expression

Yes, there is a way. In this case, it's probably easier just to use Boolean logic. Combine ANDs and ORs with the right level of parentheses nesting, and you can do pretty much anything in SQL.

SELECT c.company_code
     , c.com_inactive_flag
     , e.emp_no 
  FROM company c
INNER
  JOIN employees e 
    ON e.com_code = c.com_code 
   AND (
         ( c.com_inactive_flag = 'N' 
       AND e.emp_status = 'A'
         )
      OR ( c.com_inactive_flag = 'Y' 
       AND e.emp_status IN ('B','C')
         )
       )

Note "Boolean logic" is named after George Boole, inventor of the word AND