Beating down Miracle can be a real pain, since he has a LOT of miracles in his deck that make killing him take forever.
Several times now, I've used a combination of steals (since there's usually not much you can steal from Miracle besides pillars), Pulverizer, and Fallen Druid (sometimes mutates a creature with the destroy ability) to get rid of Miracle's white pillars. This can take a while, but if you manage to get a Pulverizer out early or get lucky with one of Fallen Druid's mutations and you're wondering what to destroy - go for the light towers (steal works too). Since all 100+ of his white quanta will be wiped out when he plays miracle, if you can manage to get rid of all his white towers, it will take him 4 turns (3 per turn from light mark) to get up enough quanta to play miracle again. By the time you've gotten to the point where you're just waiting for him to run out of miracles, you usually have enough damage on the table to kill him in 4 turns.
It doesn't work all the time, but when you can get rid of all his light towers, it makes the game end faster.
Sorry if this idea has been posted before - I looked around the forums but didn't see it mentioned.