Hmm. This might be a bit of a stretch but perhaps she's sending them to this dungeon specifically to get rid of MC but keep FMC alive?
If he dies because of something technically not directly related to the government then there might be enough "goodwill" left between the gov and FMC for them to take control of her, be it through coersion or force once she's technically alone without an ally and reason to keep fighting.
Though miss fed could just be glaring because she overheard their plans and is counterplanning to screw them over during their investigation of the disappearances. Anywhom, thank you for the chapter, and in such a short time from the last too.