Yeah.. uh.. Nova and a lower cost of Discord mathematically makes Discord come out sooner than Sanctuary. That's how it's gonna be for a majority of games played in such a matchup. You can build your deck however you want, it's not going to affect that. x)
However, once you do get Sanc out, it at least stops the scrambling for the rest of those turns, -and- provides good healing. It's not weak, it's just that it's less of a direct counter, which is good in its own way.