Any of the following might help:
1) A spell card which kills/maims all of a single type of enemy creature. Would nerf pharaoh/firefly queen decks and boneyard in addition to all fractal decks.
2) Something that removes passive abilities. Perhaps something that removes passive abilities from both sides of the field randomly, or something that randomizes the passive abilities of all creatures on the field?
3) A "quanta bank" permanent card, into which you can hide your quanta and it can't be screwed with. Withdrawal of the quanta occurs only at the end of the turn, so it's not available right away.
4) Some sort of card that allows targeting of specific enemy quanta colors. Would screw up miracle decks too.