From That Which Survives, maybe the runaway condition is with excess warp plasma production in Reactor 3. First, the antimatter fuel input controls were fused wide open into Reactor 3, and all other bypass controls were fused shut. Too much warp plasma will blow up the M/MA reactor(s) and then breech all the antimatter systems in the nacelles in the explosion causing the ship to blow up like a sun. Pulling the plug on the dilithium crystals wouldn't work because they needed to burn off the antimatter in Reactor 3. With the sabotage to the bypass controls, the only way to counteract the condition, is to burn off the excess warp plasma is with antimatter in the engines (Reactors 1 and 2), hence the runaway speeds. Eventually, even this countermeasure will fail and blow up the ship. Scott cuts off the antimatter stream going into Reactor 3 choking it off to save the ship. Maintenance would need to replace the antimatter input valve/controls, and with a little care to avoid the need for the bypass systems, the ship can get underway, again.