The Harkonnen get two free techs down their branch [which are unrewarding to other factions] and the first tech they complete will give them a very hard unit, valued about 3,4,1. Another tech or two will give them a 3,4,2 unit. Thus they will be building a tough and punishing armed force, but lacking in city-building and diplomatic skills.
The Bene-gesserit are not really a 'House' in the novels, nor do they build cities as such. They should be relieved of those bonds in this scenario, I believe, because they do have a compelling and distinctive 'Tech tree' in the novels that makes for a compelling civ, to play as or to play against. They would not be expansive or militarised, but would have arcane strengths and influences that other civ's could not acquire simply by taking over their cities. Their 'Wonders" would become "White Elephants" to a conquering military force, expensive in upkeep and providing no benefit beyond braggin rights. How could this be? The loss of a B-g Wonder to a non-B-g civ would be a trigger event that would replace the "Good" Wonder with a 'counterfeit' that has an upkeep cost of 10 to 20 gold per turn, cannot be destroyed, and confers no ability to the conqueror. The "real" wonder and its conferred blessing become unavailable to any civ after such a conquest. So other civ's won't want to mess with the B-g, yet they will want to barter for the influence, techs, and such they can provide. The Bene-gesserit would be a Religious/Scientific culture. They may require two or three branches in the tech tree, with two "placeholder" techs that they get free in each line (no earned units or wonders attached, just expensive for others to research). After those first two or three easily attained techs, which establish the B-g's position of influence, the other tech's in their branch become dependant on techs more specific to the other Houses, requiring the B-g's to co-operate (or at least peddle influence) with the other civ's. One of the B-g's early techs should be a very influential city improvement, maybe "Cloister" to replace "Cathedral", with a cultural influence of as much as ten per turn. In the novels the Bene-gesserit associate with all factions, though in different ways. In this mod, their cities will be "scattered among the nations". They will need contact with all civs to complete all their techs and to reach the apex of their ultimate developement. Being remote from their sister cities, they will need that high culture rating to avoid being consumed by one of the Houses. BTW, if a B-g city with one of their special Wonders does capitulate to the cultural influence of another civ, that Wonder stays intact with its blessings going to its new master, at the normal upkeep, unlike the military conquest described earlier.