At some point, it's less "Lower the control rods to decrease the rate of reaction." and more "The control rods separate the reaction into chambers. Do not let them all activate at once." I ended up messing up and activating them all, but late enough in the game that I'm producing negligible heat. I have invented the cold nuke.
Edit: Increasing the size of the neutrons made it so the reactions can finally be stopped. But they can also no longer be contained by the control rods. So I'm just setting off a cold nuke every time I fire, even with all the control rods down.