Distilling doesn't sound very eco friendly and PC clean air is the goal of the military these days. After all, this is the goal not, as Fisherman said, winning wars. 
It depends on how it is done. Here, in a modern distillation unit, the fractionated portions, separated by condensation are recovered and sent their separate ways as byproducts or diesel fuel feedstock.
In the third world, the apparatus is more primitive, and may consist of a drum in the ground, with a fire pit underneath and a hole in the top where the vapors are collected at the right smell/feel and condensed for fuel and the leftovers either vented to atmosphere or even dumped down the hill before the next batch. Needless to say, that process does not render as high quality a fuel as we are accustomed to, but it runs parts of the world well enough.
Properly conducted, the basic, pre-additive fuel is one of the simplest to make.
Our enemies won't be worried about using surplus fryer oil or green tech, they will be focused on winning the war, a process which isn't eco-friendly by its very nature.
