That shyt has happened in the books already. When there is no clear heir or the heir doesn't want the throne they will call on all the lords of the different kingdoms to come together to decide who will rule. It usually ends up messy.
I can see Jon killing Dany in the books and then going up north and leaving everyone else to figure it out.
Exactly. It doesn't end in a traitor convincing all the lords to support a cripple that nobody knows as king.
Jon killing Dany is probably the third major twist/shock that Martin told them. But how we get there will be extremely different. Namely, Cersei won't be queen. "Aegon" will be king, and likely burn parts of the city (via Connington). I could see Aegon being somewhat popular given his education and training. Meanwhile Dany will be seen as a mad queen at the head of a savage army.
Only thing I wonder about...how does Martin have time to get Dany back to Meereen to defeat the slave armies (or possibly free the city again, if Barristan's army is defeated by the slavers)...
...then get her army on ships heading to (presumably Dragon's Stone)
...then get her to the north somehow, after hearing about the undead
---then go through a major battle with the undead, presumably
---then get her to KL to deal with Aegon
etc etc
I've been thinking about something for years...at what point in TWOW will she even get to Meereen? Halfway? If so, wouldn't the book end with her on ships heading to Westeros? Meaning the last book would have to do some very heavy lifting and have great pacing to do everything she needs to do.