I just realized the reason the Witness removed Mars and Mercury from the system may have been to give the darkness-aligned members of the Nine the advantage so that they could work in his favor. Initially, the the Nine that were on the side that supported helping humanity (IX, I, II, III, and IV) had the majority (5-4). By removing two of the 0lanets from the inner orbits, the outer orbits that are more focused on finding a way to break free from their dependence on sentient life (V, VI, VII, and VIII) would have the advantage (4-3) and would likely help the Witness in his plan to remove sentient life from the system.