Deleting users from your Base account is a two part process that involves both deleting the user from your 'Manage Users' section and downgrading the number of seats on your account. To downgrade the number of users of your account go to Settings, select 'Plans and Pricing', click 'remove' and then input the number of seats you would like to remove from your account. Once you have downgraded the number of seats you will no longer be billed for this user.
Note: If you add a new user to your Base account they will automatically be assigned to an empty seat if there is one available. If there is no vacant seats available a new seat will be created.