After tailing a spire for several minutes (yes, minutes) multiple times in a squid, each time with constant flame/light carronade fire, taking no fire, it seemed to me that with even a moderately competent engineer, a ship can defeat the flamethrower.
This may not be a deep-in-the-numbers solution, but destroying a component currently douses the fire. Perhaps the fire should continue through to the hull after the armor is destroyed, rather than being extinguished? This would put a little more damage on the hull, and make balloon attacks more dangerous, since to effectively combat ground collision damage you would have to extinguish the fire and repair the armor, rather than letting the sequential armor failures extinguish the fire for you.