It might be just me, but after several experiments, even just enabling/disabling the BGR option prevent that. IMO it is not possible anymore to just assassinate the family tree over several turns. There seems to be a script-snippet leftover that does prevent that. (I hope you are playing without BGR, else my theory is a massive fail!
)
In one of my first SS 6.4 games, exactly the same happened while playing England and being at war with France. He had like 7 provinces, was at war with what t.F. I know of and I conquered Paris and then *booom* everything went rebel. BGR seems to spawn at least 1 family member in the next turn (in some really weird locations sometimes) or just attaches family members amongst some armies outta nowhere. So if you don't finish off every single leader/heir/fam.member in 1 turn...they just won't go rebel (*yeah*)
As mentioned, I have a damn big imagination
[it was even more obvious in my failed Teutonic campaign...the AI just boldy spawned family members and factions leader right out of a settlement I was besieging. Or in another 'experiment' after I surely got one faction with only 1 god-damn province left, down to only the FL...next turn went BAM, and 4 family member & Heir magically appeared outta nowhere. After 20~ turns, you can't say they did it like space-*****ing rabbits with lotso hormones involved, so the 1 year old child suddenly went *poof* and became a 16 year old family member]
I like the princess-theory though