When you are going back through the "Attack On The Control Room" stage, your objective is to destroy all the generators. The moment you or your partner gets close to the last generator, the flood will kill you.

Instead, exploit the co-op system to your advantage. Notice that on co-op, when one of you is further ahead then the other player, the lagging player is warped ahead. At the hallway before the last generator, spend a moment and practice finding the warp spot, now when you're sure you've located this spot have one player stand a step away from the spot that will cause the other player to warp.

Have the player that will warp go deactivate the last generator. Now as soon as the surge occurs, have the player in the hallway cause the warp and both players can leave relatively unscathed.