Oh that's so sad. If she is a first time mom, that can happen with lots of animals. I've seen a rabbit get stressed by being a mother the first time and eat a whole litter of her own babies. So it doesn't mean she'll never be a good mother. But it sure is a good thing that you took the babies you did from her or I'd hate to think what would have happened. As far as the thistle being poisoned, it's a very good possibility that is what happened. I've seen my ducklings eat thistle eventhough it had little thorns on it. I sure hope you have better luck with the next clutch.
