I haven't read any of the post-mid-2011 Halo novels. I did pick up Thursday War out of curiosity and wanted to gouge my eyes out after reading it. I'm basing that statement upon how you described it. Oh, and don't count 05-032 out of the picture just yet. When Truth arrived at the Ark, he brought with him one of the fragments of 05-032, which reintegrated with the fragment on the Ark and brought it out of its pseudo-systemic lockdown. As we can see from the terminals in Halo 3, 05-032 has a decent amount of control over the Ark's systems. If the Chief is indeed on the Lesser Ark, then it's not unreasonable to think that this may be a defensive construct under the control of 05-032.