While you cannot delete an agency from Greenhouse, you can deactivate an agency and keep it from appearing in your active agency list. Before you can deactivate an agency you must first disable recruiters associated with that agency.
Disable an agency recruiter
Go to the Agencies page. (Configure icon 
> Agencies)
Click on a recruiter's name (not the 
symbol).
Click Disable Recruiter and confirm deactivation by clicking the Disable Recruiter button when prompted.
Deactivate an agency
Once you've deactivated all recruiters associated with the agency, you can proceed with deactivating the agency.
From the Agencies page, hover your cursor over the name of the agency you would like to deactivate.
Click Make inactive, which should appear next to the edit pencil
If you need to reactivate a deactivated agency, please visit: Reactivate a deactivated agency