You shouldn't have done that.. this link is created as part of the RPM's postinst and once you run kaltura-base-config for the first time, /opt/kaltura/app/configurations/system.ini is created.
Anyhow, to correct it, run:
# ln -sf /opt/kaltura/app/configurations/system.ini /etc/kaltura.d/system.ini
and then rerun kaltura-config-all.sh and let's see..