You need update database directly to purge the record of a deleted organization.
Though the direct update to the database is not recommeneded yet if you are stuck then follow the following process and ensure that you do not do this in the higher environment until fully tested in the lower/dev environment.
Step 1: Remove the deleted organization rows from the following tables ( if there is any)
[ARCMNKEY]
[ARPFCMNORGCONFIGSTATE]
[ARADMINPAFCONFIG]
[ARUDSREPOSITORYUSER]
[ARUDSORGREPOATTRIBUTES]
[ARUDSORGANIZATION]
[ARUDSLDAPREPOSITORYCONFIG]
Step 2: Restart the web server hosting the arcot admin console web application.