There will obviously be a separate backup battery that can get you out of trouble, pretty much like the VFR and IFR reserves we have to contend with today in fuel. I think that will also be placed completely away from the main battery in the aircraft, should a fire or something catastrophic happen to the main. At least that's how I'd design it.
And look at this - a hybrid 737-800?
Flying Hybrids! - Technologue - Editorial - Motor Trend
As a complete side - just read that Toyota has sold more than 1 million copies of the Prius now. That's a huge success by any standard. Does anyone really think that any all fossil fuel driven vehicle, be it car or aircraft or boat, has any long term future?