It doesn't seem like there's any way (besides very invasive Harmony patching) for me to control when the faction gets spawned more than it already is.
I think that from a "lore" perspective the current situation is fine, as the cabal is an organization out in the world and they are active in some ways. The idea is that before researching psionics, you're like an ant to them, and they'll crush you because they can, but once you have, you're an active threat that needs to be quelled. From this perspective, I think it's alright for them to show up from time to time in other, non-direct capacities.
Of course, from a balance perspective they're still brutally hard which is why they don't spawn early, and anything that spawns them early has the capacity to totally destroy the player.