I managed to talk to one of SW:TOR writers (or to be more specific: exchange mails with him) and it seems that they indeed deliberately changed the Foundry's ending. They want to have a possibility of adding Revan later on if they feel he fits somewhere along the story. There is still hope!
Please do this.... I'm okay with the idea of killing the character, but make him a bigger deal. The final boss in an expansion, a recuring quest giver for the Republic and long term nemisis for the Sith.
Though to be honest, they should have left him in his own time.