I agree with ccoryjohnn. Nanny stealing is another issue to worry about as well as cannibalism. I wouldn't use her as a nanny, especially if you really care a lot about this litter- if its really important to your breeding goals.
It could have been a lot of different things that caused her to eat em. Too much noise or environmental stress, her or the babies could have been ill, she may not have known what to do with them etc, etc. If you do decide to use her as a nanny, make sure you leave the newborn mice alone for extra long (3-5 days maybe) and make sure they have plenty of food.
Unfortunately there's not a whole lot else you can do to assure that she won't eat them, besides keeping her out. If I were you I would try breeding her once more and put her with an experienced doe as a nanny. If she eats the second litter, you might be out of luck.