Forgive me if I'm wrong, for I don't have a N9 myself, but doesn't Aegis prevent modification of files owned by root, even by root itself?
That's because its not added to refhashlist; check refhashlist and other files have their hashes in there (cat /var/lib/aegis/refhashlist | grep etc/network) The hash needs to be added and then refhashlist signed; if in open mode adding the hash w/o resigning would work too Let me know how it goes