I had an idea to have them team up at least once before the 'separatists' emerge.
I plan for the monitor of this installation, 656 Blissful Bolt, to be more cooperative than 343 in explaining the idea of the halo rings and forerunners as not bring 'holy'. In fact, the monitor will take everyone's weapons and teleport them to the control room, ask the Spartans to politely not move, and let Lak activate the halo ring. Which, of course, won't work. This installation also did not catalog flood, and instead has cryo tubes filled with ancient species embryo's in a stasis like setting...it was responsible with choosing what races to revive beyond the humans. This ring's monitor has a unique personality that allows him to be creative, at the cost of processing speed, making him think barely above a human AI (or Ancilla/construct, as the forerunners call them).
Sound good?