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I too would create the major houses as Group containers with the minor houses as Groups contained within. I'm not sure I'd use government groups though. Maybe the top faction or alliance level. I'd like differentiation between criminal, military or commerce or whatever. And if these are inherited noble houses you may consider family groups. One reason is you can quickly see how much "power" a faction has in a certain area at a glance -- one faction has a single commerce while another has six tells you which one is going to suffer most from a naval blockade.
I would link Individuals to these houses through relationships. And by the nature of political intrigue campaigns, that's going to get messy. I'd recommend one (or more) links for loyalties plus public/private viewpoints for each.
I would not contain the Individuals in the houses unless you plan to treat everyone as property. Marriages, divorces, adoptions, orphans, hidden heirs could be a challenge with containers and may reveal connections you don't intend to reveal.
I'd set the Cast Lists up by major faction or groups of houses. And I'd place Individuals in these factions based on what their public leaning is (even if they secretly are movers/shakers in another faction). If the groups are large and fluid, it's good as they can move back and forth without causing alarm to the players.
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