The weird thing about the logic of killing deserters is that if they never joined the military in the first place they would not be shot (either by the enemy, probably, or by the "good guys"). So yet again the only winning move is not to play.
There's all kinds of terrible underlying aspects of this whole process. Young people aren't informed about the political reality of the world - they are taught a false, ridiculous version with demonized enemies (evil terrorists) and noble heroes (freedom fighters saving the world) and just like every other young person in the world, they trust the people telling them how the world is.
So then they get into the military, examine the actual world close up, often for the first time, and find that there's no relationship between it and how they've been taught. Then they weigh their options within a system designed to seduce and destroy them and select "desertion" as the best path. And then, hopefully according to such people as Kopikatsu and Post Tenebrae Morte, they are murdered for recognizing reality and acting on it.
But let's take this the next step. Let's encourage more people to join the military by destroying the domestic economy, thus rendering military service the best economic path. When coupled with deluding people into noble fantasies regarding the role of their military in the world at the very least when they finally wisen up and choose desertion they won't have a decent economic situation to return to, even if they escape the hail of bullets fired by the "good guys" on the way back.
The best way to get someone to enter a meat grinder is first to delude him into thinking it's wonderful, second to threaten him with death if he ever becomes un-deluded and third, to make sure his other options, such as civilian service, are so economically devastated that the meat grinder looks reasonable in comparison.
Remember, kids, we're the "good guys". Don't let all the manipulation, seduction, terror, fear-mongering, threats, heroic fantasies, and devastation ever incline you to believe otherwise.