Here is an idea from Crusader Kings 2 that we can borrow:
Let the Family/House of each player get its own honor and prestige values. Every time one of your nobles die, their honor and prestige get added to your Family/House's honor and prestige. This is the only way to make your Family/House's honor and prestige increase. The honor and prestige for your Family/House do nothing. They are just for bragging rights and "high score" comparisons.
Existing dead nobles can have their honor/prestige retroactively accounted for, assuming that the game still remembers them.
Possible exploits: People could make a bunch of nobles and then delete them. Maybe make it so that retiring a noble that you've played for less than a month does not increase your Family/House's honor and prestige.