You were right - each character has a hidden tag in addition to their shown tags (mystic/scholar/etc) called "AVATAR", which is only present on players who are there from the start. I added that tag to our Fane character, and the initial look is good - he can't be booted from the party!
I used the tool found in this thread: http://larian.com/forums/ubbthreads.php?ubb=showflat&Number=572322&page=9
I'm not sure how this'll affect Godwoken quests though. . . kinda sucks that he's an Origin character, since that means there are probably some quest flags that might specifically only be present in a game with AVATAR Fanes (instead of Companion Fanes). . .
It would be awesome if I could get my hands on a save file in which Fane is an AVATAR and past act 1, so I could analyse it for any unique fane-related quests ours might be missing. . .