The new cobbler (2.x) uses rsyncd for replication with the native rsync protocol I thought. Michael mentioned removing support for rsync over ssh due to key problems. You can control the user that is ran on the remote side by changing the rsyncd.conf template. Forgive my ignorance, but does cobbler 2.x support replication over rsync/ssh?
I would have thought so, the piece of code that's responsible for syncing is still there...
Using native rsyncd will impose additional problems, like rsync port being blocked on firewalls, whereas SSH is usually open. I think rsync/ssh should remain available as an option.