I think fractal and miracle are fine as they are.
The main point of them draining your remaining quanta isn't so that you can't use any aether/light card that turn, but so that you can't stockpile a lot of quanta and then use fractal and miracle multiple turns in a row. The god Miracle can spam miracle because he produces over 12 light quanta per turn, but many rainbow decks with eight pillars would be lucky to produce 3.
Draining all quanta would hurt any deck using these cards that's not mono. This would include Decay, Eternal Phoenix, even Rainbow. And as you have said, no mono uses fractal or miracle anyway.
If you can think of a more reasonable way to nerf them, feel free to suggest it. But I think they have been balanced well in design.