The way I see it the UNSC (ONI) don't understand Halsey's true purpose. [spoiler]They do not know she was created by the Librarian, so the librarian could put her plan into practice, kidnapping John and creating Cortana. Cortana to guide John to his destiny as he has Forerunner DNA and may actually be a Forerunner. Halsey is just a scapegoat and a plot line to bring Jul'mdama and Agent Long into the picture. I think Long will seek out the Arbiter to learn how to either stop or assist John. Who knows, Lasky could have reprogrammed (genetically) Long to save the Chief from the UNSC rather than kill him or capture him as they wanted. UNSC may know more about Chief than we thought. With introduction of the Didact they see Chief as a threat? [/spoiler]