Remove permissions ->Remove All permissions should remove users from groups with permissions as well
Users would expect removing all permissions for a user to remove that user from any permission group. At this point, to completely remove a user from a site, you have to run remove permissions->Remove from Existing Groups, and then run this another time, but this time "Remove All Permissions". It seems the latter should also take care of removing the user from groups. At least it's what a user would expect.