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 Agency Recruiters
From your Dashboard, click on the Sourcing tab, and navigate to Agencies. Click on a recruiter's name (not the 
symbol) to access the page where you can manage the recruiter's access. This will open a page where you can manage the recruiter's access.
Click Disable Recruiter and confirm deactivation by clicking the Disable Recruiter button when prompted
Repeat this process for every recruiter within the agency you wish to deactivate.
Deactivate Agency
Once you've deactivated all recruiters associated with the agency, you can proceed with deactivating the agency. From the Agencies page (Dashboard>Sourcing>Agencies), 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