I'm still puzzled. My yun was not as up to date as yours. I've updated it. opkg is still successful
root@Arduino:~# opkg update
Downloading http://downloads.arduino.cc/openwrtyun/1/packages/Packages.gz.
Updated list of available packages in /var/opkg-lists/attitude_adjustment.
Downloading http://downloads.arduino.cc/openwrtyun/1/packages/Packages.sig.
Signature check passed.