Correct - you'll need to be organisation admin in a Premium (paid) organisation on Podio. The organisation admin will have access to the User Management page and control the organisation from here: https://help.podio.com/hc/en-us/articles/201019828-User-Management
You are not charged "free spots" based on the employee directory - only on employees invited to workspaces.
You can remove the member from workspaces if you are workspace admin, go to the workspace, click the wrench icon above the workspace activity stream, then choose "manage members", now click on the member you want to remove.
You can also ask the member to leave the organisation. They can click the wrench icon next to the organisation name, then choose "Leave organisation". Could this work?
Sara - Podio