tbh, i think junho ran because he had enough--he just realized that after everything, no one gave a shit that seokbong killed himself. at the end, training continued and the soldiers weren't even allowed to feel "gloomy".
the show itself is a commentary on the brutality of the military, so it makes sense that ultimately, the one who is supposed to bring back the deserters will desert. even the officer in charge was constantly worried that they would desert when they were out, knowing that deserting might be better than staying. imo, it was all foreshadowing his final decision.
the "enemies" or the bad guys were always the bullies and not the deserters. once junho realized that bringing them back wouldn't change the brutal reality that the bullies would never be charged and that bystanders would continue to just watch, he couldn't figure out why he kept doing his job. i think the author's shows that being a deserter is not inherently bad and that in some ways, it's a brave act. so i don't think it's unreasonable to believe he would make the main character, the hero, become a deserter himself. i read that the show is based on the author's own experience in the military--maybe he had imagined deserting and lived out his fantasy through junho