Talk with the school counselor. He may be able to give your daughter some individual time or include her in a small group. You'll probably want to seek additional help for your daughter outside the school, and the counselor or your pediatrician can refer you to a therapist in your community.
You may also want to consider switching bedroom arrangements. You're wise not to let your daughter get into bed with you. You might be able, however, to switch bedrooms and let your other daughter, your son, or even you and your husband move to the bedroom on the ground floor. Since this is a tremendous issue for her, it doesn't make sense to continue to have your daughter sleeping on the main floor by herself. This fear of storms may simply be her way of telling you she's frightened to sleep there.