By lore, the Lunatics shouldn't even have the contract to cause trouble for the factions until at least a few research topics into their tree, but mechanically we can't do that, I don't know if it's impossible or merely difficult, but end result is that the contract is a starting thing.
By lore, it would make sense to have trained brainers be more difficult to get, but mechanically it may be less than ideal.
If the Lore conflicts with reasonable game mechanics or would lead to something that gets in the way of enjoyment, it is liable to be ignored or handwaved. This is not necessarily a bad thing, and though I think it could be fun to mess with a less stable brainer supply, it doesn't actually sound like it would enhance the experience overall.
If it helps, that 200000 cost to get a brainer might be going entirely to a black ops group who finds a willing brainer and smuggles them out to you.
Though if anyone is actively interested in that sort of thing, isn't that what mods are for? Balancing would likely be a bitch and half, but perhaps it might be worth it.