For holometabolous insects, those that undergo complete metamorphosis, the pupal stage is the transitional part of the life cycle between larva and adult. The larvae of some holometabolous insects form cocoons and then pupate within the cocoon, but the pupa is still the transitional stage, and the cocoon protects the pupa from adverse conditions.
The process of forming the cocoon starts with attaching silken threads to nearby substrate and using that to hold the larva in place as it spins the cocoon. If the larva is unable to attach to the substrate, it will be unable to weave the cocoon, but it must pupate anyway. This makes glass a less than ideal housing in that respect; however, as long as conditions are favorable (good temperature and humidity, no mold, etc.) the pupa will still develop and eclose just fine.
That said, insect behavior is not something in which I specialize, so I don't have an answer for why she ate those pupae. I could speculate that, in nature, larvae which are unable to spin cocoons in the nest would likely have some physiological defect, so eating naked pupae may be a normal biological response so the nest can reuse those nutrients which would otherwise be wasted, but I'm not sure.
For cocoon-forming species, especially those which have trouble moving on glass, it may be helpful to put some sort of substrate in the tube for attachment or use an alternative to test tube colony founding. I'm sure others could comment on their experience with this species or Camponotus, generally.
