I would just go in and make sure that I only assign important families to be regional governors and military leaders, then put the strongest individuals regardless of family in all important government positions and research positions. It helps keeping a tab on which families are feeling scorned and routinely making sure you're changing out non-important families governing your regions. The system is definitely a bit broken, it seems designed to annoy you every time a major character dies and perhaps keep the civil war risk high. It's a feature that feels intrusive and annoying, but is perhaps sort of historically correct