Create a membership list with employee name
To get the employees, run an advanced search.  In the relationships section, select the relationship type and enter the organization that the employers are related to.  Then, go up to the top section and find Display Results As.  Select "Related Contacts" and then in the relationship type drop-down that appears, select "Employee Of".

You should get results of all the employees.  Create a smart group from this search, and have your directory profile use this new group instead.

Finally, to display the employees' employers, add the field "Current Employer" (available under "Individual") to the profile, making it visible as a result column ("In selector").  (You may need to remove any organization-specific fields and/or create a fresh profile as your profile is now a listing of individuals rather than organizations.)