L.L.
Do you think she may have allergies? Or, perhaps she has dry eyes; something like artificial tears could help, but ask your pediatrician first. Could she have blocked or irritated tear ducts?
Also, maybe she's still tired, and the itching and rubbing are signals of this? All babies have different "tired signs"; rubbing the eyes is probably one of the most universal, after yawning.
Have you considered putting her in mittens when awake? Or possibly using long-sleeve kimono tops that are a size or two larger so the sleeves will be long enough to cover up her hands?
Good luck S.!