Rifqi_Fajar_Zain The main feature of flamethrowers is that they are able to ignore shields. Therefore, I will not remove this ability. It is possible only to increase the price of this flamethrower. Use the weaknesses of flamethrowers to fight them. Build a ship using the not-flammable corridors and modules. (in the next technological levels there will be more and more not-flammable modules.) Fight flamethrowers from a long distance or from other flamethrowers, install more fire extinguishers.
Note that the higher the technological level, the more powerful can be his weapon. Therefore, with the increase in technological level, improved weapons will be more overpower standard weapons.