I just started playing Stick of Truth this week, I have run into precisely the same bug with the same cause (I saved the game just after rescuing Cornwallis and later reloaded). By the time a realized my error, my only save files before the bug were before the alien space ship quest.
I have attempted to return to Mr. Hankey but it won't recognize that I have completed the quest. The quest is marked off in my journal, but Cornwallis was never added as a friend.
Is there any kind of bugfix? I don't suppose this game takes console commands that can reset the quest?