Based on what we've seen so far:
Out of universe:
The shooting we heard and saw at the end of the episode was clearly intended to make us think that the people who had been taken away were being killed. I suspect that Nick isn't dead yet, because he was such an important character, and it just seems too early to kill off main characters. I don't know how else to explain the shooting, but I am reasonably certain that we'll find out before the season finale.
In universe:
Although the fate of the "deportees", for lack of a better word, is unclear, it is absolutely certain that the military has been killing uninfected civilians. When Madison went outside the fence, we saw at least one person who had been shot down while apparently uninfected and holding a semiautomatic handgun. When she returned home, she spoke with Daniel.
Daniel asked "What did you see?", to which she replied:
"Bodies. The infected. There was a man, shot like the others, like the rest, but he wasn't sick. And there were others like that."
Daniel, a survivor of the conflict in El Salvador a few decades ago, clearly understands what is happening. He relays a story about his childhood. Men from the government came to his village and took some people away. His father, who was apparently serving in a similar capacity to Travis, asked the military where they were being taken, and the officer told him "Don't worry, they always come back". A short time later, Daniel was fishing in a nearby river when he found the corpses of the people who had been taken away, either floating around or submerged in the water.
Daniel then gives Madison some insight into their current situation:
"My father told me not to have hatred in my heart. He said 'Men do not do these things because of evil. They do evil because of fear.' And at that moment, I realized that my father was a fool for thinking there's a difference. When it happens, it will happen quickly. Keep your son close."
His words proved to be remarkably prescient: That same night (if I'm not mistaken), the military came to the Clark/Manawa household and took Nick (who is indeed Madison's son) to an undisclosed location, against his will and the will of his family.
Is there an evil plot?
No, it seems to me that the problem here is the lack of any well-thought-out plans. Communications are already breaking down, and we seem to be seeing a distressing amount of improvisation. The military has presumably been ordered to take out the zombies, and probably to deal with any potential unrest, but the unit running the camp where Madison and her family live appear to be exceeding their briefs, and showing a remarkable degree of autonomy and an increasing lack of prudence, restraint, moderation, and self control.
As I see it, the issue isn't an evil plot; rather, it is an apparent lack of any kind of planning.
Speculation:
The obvious implication of the episode is that the military in charge of the safe zone is probably losing contact with high command, and rapidly devolving into a tinpot dictatorship. I am almost certain that this state of affairs will continue on its present course. As the bureaucracy breaks down, the officers in charge of each of these little camps will be left to their own devices, and although many of them will probably do their best to uphold the standards of conduct instilled by the military, many others will be less scrupulous, and will become tyrants over their absurdly small "kingdoms".
We've already seen this happen in the original series: The police who kept the hospital in Atlanta operational, to some extent, became despotic and cruel, abandoning the morals that guided them prior to the end of the world. The same thing has already begun to happen in the neighborhood where our protagonists live, and I don't see any reason to doubt that the devolution will continue, and even accelerate, as the government loses control of the situation and is steadily eaten away by the innumerable hordes of zombies.
I think the writers and producers are giving us a glimpse of things to come, and a disturbing indication of just how seriously the situation has already eroded.
I'm reminded of the famous footage of then-Lieutenant General Charles Honore entering New Orleans after Hurricane Katrina. He saw a truck full of soldiers driving by. The soldiers were holding their rifles up, ready for action, as though they were in Iraq rather than an American city. The General shouted "YOU ARE IN AMERICA, NOT IRAQ! I WANT TO SEE THOSE WEAPONS POINTED AT THE GODDAMN DECK [i.e., the ground]!" No one is saying that on Fear the Walking Dead. No one is reminding the soldiers that they're on friendly soil. This can only lead to a catastrophic breakdown of discipline, with horrific consequences for the civilians who are ostensibly under the protection of the military.