The most important thing you can do is to pray for her, and to let her know that in spite of what her teacher says, many outstanding scientists believe in God and see no conflict between their science and their faith.
Just this week, in fact, I read an interview with one of our nation's leading biologists. As a young doctor, he considered himself an atheist but he had to admit that Christ made a difference in the lives of some of his patients. He knew that as a scientist he shouldn't be close-minded but should investigate the claims of Christ for himself. When he did, he became convinced the Gospel was true and committed his life to Christ.
Encourage your daughter also to grow stronger in her faith through prayer, the Bible and fellowship with other Christians her age. Situations like this can shake our faith—but they also can strengthen it if we realize our weakness and turn to God. The Bible says, "Consider it pure joy, my brothers, whenever you face trials of many kinds, because you know that the testing of your faith develops perseverance" (James 1:2-3).
As a footnote, I suggest you talk with other parents about this teacher's attitude. Ridiculing a student for his or her faith is out of order, and a quiet word from some of you to the school's principal may be appropriate.