What happens if the Tragedy at Summerhall results in the wholesale destruction of House Targaryen (Aegon V, his former heir Duncan the Small, his current heir Jaehaerys, the heir-in-waiting Aerys, and the newborn Rhaegar, along with any wives, sisters, and cousins in attendance)? TWOIAF hints very strongly that the conflagration would have been even more devastating but for the valor of Dunk. Do the lords call a Great Council to find an acceptable candidate or does the realm simply fracture?

Yeah, definitely a Great Council. I think the fear of total instability would probably cause people to hold back from separatism initially – especially since, with no monarch, no fresh grievances. 

However, what happens next is completely up in the air and might well fracture the realm. If the Martells and Baratheons clash over which of them has the closest links to House Targaryen, if there’s not a clear consensus candidate or if the debate drags on too long, if Maelys invades with the Three Daughters behind him, you easily could have the realm fracture.