Could be, but also the flood could have been there for research purposes and the flood managed to overwhelm the halos (coming from elsewhere) , making it impossible to release them. OR maybe the flood put them in stasis to allow them to survive the activation.The "samples" (Flood) stored at the "Research Facilities" (halos et al) are there to give whomever came next the one thing the Forerunners lacked: time. A head start.
And yes, hte covenant released the flood during Halo: CE