I've never seen a hint of the dynasty system affecting the fallout from an AI sovereign going down.
see the explanation of dynasties as given by Brad (frogboy) at PAX 2009.
He explained in (I believe all) the elemental talks and at least one of the general stardock general talk that when Sovereign A marries all his children to Sovereign B, then Sovereign B is killed by Sovereign C some of Sovereign B's land is inherited by his next of kin which is the offspring of Sovereign A, so suddenly Sovereign A who has been diplomatic and non-aggressive the whole game owns half the map because he inherited it.
The exact terminology and phrasing I do not have, so the above is a paraphrase not a quote. But I'm sure with very little digging you should find it. If you can't just let me know and I'll dig it up for you.
Its like... the reason the dynasty system exists as far as I know. I think they just didn't get all the features in yet. (by 'that' I mean as a method to expand and eventually win through diplomacy)