If the lithium is contained it will not burned. Lithium ION is not as bad as Lithium. Some newer polymers are not as bad either.
In say a laptop the cells are pretty well packaged themselves. After the package they are then in a pretty tight plastic battery case. You can do anything you want until they burst. When they burst they can make a small pop and start oozing and smoking or in the case of say a short circuit, they can dump energy fast enough to blow it right through the keyboard.
If you have a battery which is smoking it has likely lost containment. You fight a fire in an aircraft with Halon because it's well all you have.
I always look at operations as odds. Can you get away with it once? 100 times? 1000x? 100,000 operations per day? what is acceptable risk? If this was a discussion of only a 1000 flights it wouldn't even be a topic of discussion.