Not only do you have to consider the rewards you'll be handed by assigning Facilities to either the Survivors or Peacekeepers, but also their ideologies and the overarching narrative. If you agree with one faction more than the other, then that can trump any rewards you could receive in-game.
For our own playthrough, we assigned Facilities to the Survivors. They welcome you in (eventually) at the Bazaar, and we were more interested in rewards to parkour rather than combat. As a result, we recommend assigning facilities to the Survivors. However, going with the Peacekeepers instead is just as much of a viable option. Maybe you'd prefer those sweet combat rewards instead.
Don't forget that if you're looking to unlock the Boot Licker Trophy, you must prefer one faction over the other and assign seven Facilities to either the Survivors or Peacekeepers in order to unlock it.