Don't know much about scripting events but the best way IMO would be an event "legitimize Jon?" and then if the heirs are wiped out Jon spawns as faction leader.
Not sure since when you mean but the Night's Watch and Wildlings + the Dothraki are added even if they have few units and the current map doesn't really give them anything to do. Won't be adding more factions for this version I think, the ones already in still need work.
EDIT
Two new units in progress. Started doing the Glover last year but lost the model, felt it should be included anyway. And the Mormont cause I like that shield I guess.
Attachment 346551
May not be able to do all the characters I planned, I think I may have overstretched a bit on that point. Will have less time to mod going forward too. Still, the following generals are done or basically done: Robb, Jon (BotB), Rodric Casell, Thron, Roose Bolton, Tywin, Jamie and Tyrion Lannister. I'll try and at least get Stannis done though.
Fixing bugs and getting the above into the game along with the Lannister units from the trailer is what I'll try and do next. Nygren is putting the units into the campaign files atm. I think the mod should be released around the premiere of season 7 instead of at the end of it personally, I probably won't be able to add stuff from S07 until the holidays anyway. I think it depends on how stable the mod ends up being...