Counters:
Silence is a direct counter to this card. Play it once they are in deckout-prevention, and they are screwed. You will have no cards in your deck (unless you play more than one of the card, in which case your opponent just took 14/12 damage, and if your deck can't win with a 14/12 HP advantage, you need a new one)
Simple damage always works too. They will take 7/6 damage per turn with this card, so they will be more vulnerable.
Sorry, but it is staying a spell. A permanent form would be too vulnerable (increasing the possible counters to include Pulverizer and Deflagration), and that isn't what I need when there is already Eternity + Photon, which is a deckout with all of the same vulnerabilities (Deflagration, Pulverizer, Silence, and simple damage) but does not reduce your HP and is also powerful CC. This card's advantage over Eternity + Photon is that it is more reliable (cannot be destroyed with Pulverizer or Deflagration) and accelerates quanta production (one Darkness Pillar / Tower per use), but accelerates your demise through damage (7/6 HP / use) and does not also function as CC (like Reverse Time).
It has its own strengths and weaknesses purely because it is a spell and not a permanent, and changing it to a permanent would upset the balance.