The one-world-one-vote system will actually advantage the recovered Marik-Stewart Commonwealth worlds. The old system assigned votes based on GDP, but any planet that's transitioned to a clan economic system has seen it's GDP plummet (because a lot of the economic activity would have been deemed 'wasteful' and shut down). That's on top of those worlds having been violently conquered an having had their trade links to the rest of the FWL severed, each of which could cause an economic crash on its own.
The newly empowered aristocrats might not like the Halas line right now, but Halas blood, treasure and legal wrangling will be responsible for them gaining political power. That kind of thing tends to change a person's loyalties. What has house Marik done for these people in living memory again, other than fail to protect their interests?