As with any design and the components and the manufacturing and finally the actual implementaion/fielding, things show up that nobody had considred.
Apparent;y, the Boeing warning system alerted the crew (Nippon emergency landing) that the battery was getting hot.
I have no problem with the Li-ion batteries. OTOH, I also believe that using them in an airliner should have really good charging systems and monitoring systems.
The only problems I have are related to the effects of the thermal runaway characteristics. Saw a BMW or similar catch fire one night after a fuel leak caused the driver to pull over and then grab a fire extinguisher. I couldn't do much and neither could he ( no cell phones back n late 70's). Next thing you know is the transmission casing start to burn - aluminum/magnesium alloy. Fire department showed up, but once that metal started to burn all was lost.
So my feeling is Boeing will add some fire protection capability and also look long and hard on the battery charging/monitoring circuits.