This question is one I have contemplated off and on for a while in the context of Clan Wolf's move from their OZ to the Lyran Commonwealth. Just who and how many of the civilians in their OZ would be accounted, and account themselves, as members of Clan Wolf after nearly 100 years of occupation? How integrated were the civilians of IS and Clan origin in the OZs? Answers to this question would go a long way to answering questions about the scope and scale of the Wolf migration. If the entirety of the civilian population in the Wolf OZ was considered part of Clan Wolf then the migration had to evacuate a portion of billions of people. If only those of Clan descent and those that had chosen to join or were adopted are considered part of Clan Wolf then the Wolves may have been able to evacuate a large proportion of their Clan to the LC leaving behind only those non-Clan IS inhabitants on their OZ planets. There have been portions in books like the Field Manuals, Era Reports, and Bonfire of Worlds that support each interpretation, though they do seem to me to be leaning toward the more integrated interpretation.
Clan Wolf under the Crusaders weren't quite as nice to their civilians as the Wolves have been historically, however at least part of that may have been due to the losses, and pressure the Crusader Wolves were under almost continually from 3058-3085. As well as, Clan Wolf having to depend more and more on the Wolf OZ to support the Clan, especially after ~3071 and their ejection from the Homeworlds.
As to the lack of rebellions and the seeming support for the Wolf Empire. First, the Empire has promised peace and security in a time of fear and instability. A promise the Wolves have, so far mostly, been able to keep. IRL people have been willing to give up a lot for the promise of security. Second, look at the alternatives the people have tochoose from in lieu of the Wolf Empire; the Jade Falcons, Lyran Commonwealth, Free Worlds League, and Republic of the Sphere. The Wolf Empire is a haven of peace and prosperity compared to all the others. Fear of Falcon war crimes as much as anything is probably keeping most of the people cooperating with the Wolf Empire. The LC and RotS have both shown themselves to be unable to deal with the current Dark Age situation and have been unable to defend their worlds and citizens. The FWL is inherently unstable and its current incarnation is still young and unproven. Also, Alaric Ward's ancestry, as well as, the Lyran's ill-handling/betrayal of the Wolves is likely played up in Wolf propaganda in the Empire to get the people to support the Wolves. Finally, there are issues with the volunteer Galaxies, Mu being the most prominent case, being merely unreliable at best, and near mutinous at worst. Any Wolf officer that tries to keep the unit in line quickly winds up missing or dead.