I think it might be possible to disable them for Aya specifically. (Not that I really now anything about how things would be coded.) My assumption is that is has to keep an idea of what kind of bullet to create for each character when they send one of those snowflake things over. So the info for Aya's specific bullet must be written somewhere, and could presumably just be changed to nothing, or have its parameters changed so it, say, moves really slowly, or has a microscopic hitbox, or none at all. So the snowflakes would still fly, but what comes out of them would be different.
Though making the AI invincible is a nice idea. Probably much harder to do though, yeah. I've wondered why ZUN didn't just make it that way to begin with, and I guess it's to make it seem like you're actually "fighting" the AI, rather than just surviving. It would have been nice.
And now I'm just sitting here wondering, if I had the know-how, what kind of madness I could mod into the game. A man can dream...