I still don't really see this as a problem. We should try to balance at a faction level, not a mechanic level.
I agree though that some of the obvious bonuses (Slig, Caladaanian wine) should be faction-tied.
But I see no reason for Harkonnen to be tied to a particular resource. Offworld labor is the only one that would make sense for them, but that is the most useless to them, because of their slave mechanic.
Are you guys unable to add any more resources? I'm somewhat curious since it seems your arguments seem mostly based on using current resources, rather than adding or substituting other types of when the system is reworked. (which from the recent posts in here seemed something you're considering anyway.) If nothing else, there also aren't enough resources in game for all factions to get a couple. (18 needed, vs. 9-11 or so in game, I don't remember exactly.)
In greater detail, the issue here is the forced specialization that tying a faction to an automatic world resource would cause. Having the harkonnen not be forced into a particular contract doesn't just mean they don't automatically have a particular resource, it also means they have a lot more gameplay options for the resources they do get. This isn't an issue as much if the house contracts aren't forced, but is an issue if they are. (This sort of forced specialization vs. a more generalized use also seems funny backstory wise to me, although I'm not sure about other people, though gameplay wise it certainly seems really off.)
(I can see the individual points of what you're arguing, it's when they get put together that the result doesn't work well.)