Some posters seem to be commenting on one of three separate scenarios:
a) a phone battery fire in the passenger cabin
b) fire among bulk cargo of lithium-ion batteries in the hold
c) fire in the 787 main battery.
The original post is about a), of which several occurrences have been reported - usually resolved successfully by dropping the offending phone into a bucket (or other convenient container) of water.
b) should not happen if ICAO recommendations are followed. I suppose an alternative solution would be to build in "bomb doors" so that burning cargo, of any description can be dumped (avoiding, of course any schools, hospitals or other socially sensitive establishments).
c) has been mitigated by putting the battery in a steel box, vented to the outside. Two batteries, well separated would provide additional security, but I believe all eggs are still contained in a single basket.