This may have been brought up before the beta came out, but creating custom factions is nice. Trying to delete them and then having them come back time and time again is rather annoying. Apparently the only way to have them stay gone currently, unless this has been changed is disabling Cloud Saving in Steam. A bit of a pain just to permanently delete a faction, but I can see the catch-22. There are people who will NOT want to lose their custom factions if the computer decides to die and you need to reinstall the game. There may be custom factions you may not want to recreate from scratch.
My recommendation is two-fold. First the option of looking through and managing/deleting your custom factions. Secondly making a box called "permanently delete" so that the custom faction is deleted on both the cloud and the computer without having to search for the directory each and every time, and prevent the failed faction from coming back the next time cloud synching takes place. I know it's fairly simple to look for windows directories for many people on these forums, but there are those who will regardless be confused.