I'm sorry, I was short on time in my last post. To sum up a thought from another post which I think is pertinent here, PHALANX would not be denied any viable military technology to combat the greatest threat ever known (excepting, perhaps, those causing widespread environmental or population damage), within the discretion of the commander/player. That said, the Flamethrower is just a blip on the inhumanity scale, especially when is not intended for use on humans.
I also feel that a more imposing flamethrower effect would not be outside the theme of the game. Many fictional anti-alien forces have pursued sterilization, through fire or other means, of alien sites. Once humans begin to be infected/affected, I could believe that teams would carry a flamethrower man to clean things up (whether or not there is any gameplay significance, it still thematically fits).