The point is, if the 787 gets cleared to operated again, it will be because the FAA/NTSB/whoever decide the battery solution is safe and reliable enough.
Thus the main battery will be the back up to the brakes. Why are people suggesting or assuming the 787 will be flying around without a battery or in a perilous condition as there might be a double engine failure, then for some reason the APU won't start and THEN the (new safer more reliable) main battery will also fail?
The 787 when cleared to fly will have a backup source for the brakes as the new battery and it's associated systems will have been certified as being safe and reliable. As I ever, I expect some people have ulterior motives to scare monger but there seems to be a lot of unfounded sensationalism on this thread.