Rebellions let you appoint the council of your choice, so you can name whoever you want as judge (even yourself) and then just ban the unwanted dukes. Bans are for casting out whoever you don't want in the club anymore, regardless of the reason, not just for people having broken pre-written code of laws.
The game has been gearing towards greater respect of the feudal hierarchy, so I wouldn't see this happening. A rebellion is against the government, not against the land owners (lords and dukes). That one might need to overthrow the former to deal with the latter doesn't change this.
That being said... Sometimes the government has been reigning long enough to have had a few rotations amongst buddies and therefore some of the dukes are royal, which you cannot ban. I think it would be reasonable for the new government to be able to ban these people. It would seem reasonnable to me to give some special ban feature to rebel leaders, available for 2-3 days, that allow them to ban people (perhaps only those who were loyalists in the rebellion?).
