OK, so I gave this one a little more thought on my drive in to work this morning. Excluding bacteria and other organisms is only half the battle-- the other is excluding oxygen. I thought of two different ways to tackle both problems at once: a) a simple, elegant, and automatic solution, though untested and it would need some trials to dial it in, and b) a complex solution that will definitely work.
A) At some point before fermentation ends, attach a balloon to the BB so it will fill with CO2. During crash cooling, the CO2 will supply the extra gas needed to prevent the BB from collapsing under negative pressure. Some experimentation would be needed to determine exactly when to attach the balloon so that enough CO2 would be collected to counteract the contraction of the gas in the BB.
B) Attach a CO2 dispenser (cylinder, cartridge, etc.) and pressure regulator to the BB after fermentation is over and set it to something very low and non-dangerous (e.g. 1-2 psi) and crash cool as normal. Same principal as the balloon in (A), but less "hit and miss". Or, instead of using a pressure regulator, just use one of those small CO2 injectors and regularly apply a short burst of CO2 during crash cooling.
Of course, all of this is probably way overboard, but that's generally my MO.
-Steve