You'd phrased it as removing an object's ability to emit species, rather than affecting the species directly, which was what had me confused. I agree it should be possible to just destroy the species directly (but that the "Room" issue remains a problem).
I will assume that she didn't cast the PeIm spell, as she would have had a good enough understanding of Magic Theory IC to know that there was going to be the Room issue.
The Muto Auram effect on the clouds could work in principle (and has the bonus of being consistent with at least one of the versions of the story that was going around). Level might be tricky...
Assuming she's using her Potent Spontaneous Magic, I make her MuAu casting total:
(Mu 12 + Au 5*2 + Talisman Muto Bonus 5 + Sta 2 + W&G 2 + Aura 6 - 1 Fatigue)/2 = 18 + die/2, so she can probably get a level 20 spell before dipping into LLSM unless she gets very unlucky.
I'd say you were probably looking at the Base 5 Guideline "Transform an amount of air into something slightly unnatural)".
You'd need a Group target, and one extra magnitude wouldn't hurt - an Individual of Auram is sized a a base Boundary, i.e. 100 paces across, so Group+1 would get you something approximately 1000 paces across (assuming you're only changing the size in two dimensions).
Assuming Concentration duration on the spell, that gets you to Level 25, which is two fatigue levels down unless she gets very lucky on the roll, which is the most she can manage before falling unconscious.
You then need a Range - Sight is traditional, but that would bring you to Level 40 (and leaving aside anything else, if Viola can't rely on remaining conscious, she'll need to up the duration). It would therefore really help to be able to bring the Range down. In theory she could transform into a butterfly using the bond power and fly up to the clouds, but that's likely to be...interesting...in the storm, not to mention the problem of knocking yourself unconscious in flight.
Unless I'm missing some extras to her casting total, it feels like the only way Viola is going to pull this off short of a lucky roll is by pumping vis into it.