If there were flood controlled variants of planets, and you get the research to colonize it, then the population growth should be really, REALLY slow, to simulate the pushing back of the flood infestation on that planet. If you are unlucky, and get a planetary bonus like a Gravemind on one of these planets, then the growth is either nil or you lose control of that planet.
Or you could make those planets get a small group of flood-controlled ships (like rebels) that jump into the grav well every so often.
To balance out the incredibly small growth or small population on the infested planet, either the tax rate should be really high or there should be a lot of asteroids around it.
