Yes I did just hide them. I kept a to-do item to find out why they aren't being removed as they are supposed to be.
I made a few other minor bug fixes while waiting through various updates and builds. I'll add this one to the mix. It will be fixed in the next client update. I'll post that either today or tomorrow.
The code has been fixed to get rid of forgotten empires from empires' lists of know empires. It will require a server restart. Client was fixed to stop hiding forgotten empires. It depends on the server to remove them.