Ds does that a lot too, I have found that it is worse if I try and move his hands away or wrap him, he just gets them out anyway and runs and pulls his face harder.
The best thing that I have done is if I am putting him down awake is to put him down without blankets or anything at all. He seems to relax more, I have also stopped using polarfleece suits, because they were irritating him, and now he uses the sleeve of his cotton suits to rub frantically at his eyes instead of his hands, and this puts him to sleep instead of hurting him and waking him up!! Maybe you could try some cotton mittens....if you can get her to keep them on, at least them she may not atcually be able to pull at her eyes? DS often sleeps with his arms over his eyes!!