There definitely is the possibility of a Minority Report type thing going on, given the second victim's Talent, but it still doesn't make a whole lot of sense. Her reports are so vague. "X million" and nothing else. Nothing about who or how or when, just a number.
Assuming Touma's danger was in becoming a leader, what evidence is there that killing him would make a difference? If a young pre-Chairman Mao had been killed, would the Communists have still won in China? Would the policies of their leader in this alternate reality be more or less effective than Mao's? Would the same millions still die, or more, or fewer? Or would Chiang Kai-shek have won in this version of history? Who can say with certainty how any of these changes would affect global geopolitics, the Cold War, and so on? There is absolutely no way to simply summarize this into "killing Mao would save X million", even if you have a Talent on your side. And all these questions are only if the leader hypothesis is true.
But nothing makes sense regardless of future-seeing.
The cover-up is that the Talented are training to fight the Enemies of Humanity. OK. What does the public get told about the fighting? Where are the veterans, the medal-winners, and the honourably discharged disabled? Is the general public getting told their last, best hope is suffering a 100% combat mortality rate? And why is Autist-kun there looking for his sister? The family clearly wasn't told she was KIA against the monsters, but if that's not what the government claims how do they explain everyone's disappearances? Is there no war reporting on the supposed fighting, no after-action reports, no footage? This conspiracy has gone on for 50 years; how has it remained intact with no evidence of the fighting? If the goal is to eliminate the Talented, why make them sympathetic to the public and elevate them to heroic martyrs? What is the impact on the economy of an imaginary war, and on international politics? 50 years is at LEAST 10 governments in most democracies, so how have the different leaders and different parties all agreed to keep things going - in every single nation that would be aware of the Enemies?
And why bother with any of the murder in the first place? They're going to kill them all anyway. Doing it one at a time just gives them the chance to catch on, which is exactly what is happening. Take them on a spelunking field trip where the cave is a giant gas chamber or something. There's no way this is the first time in 50 years that anyone's been paying enough attention to notice. And how can the teachers not be aware of the situation (see Ch.4, p.17-18)? If the students are killed while they're there, how have the teachers never noticed?
It doesn't even make sense to make those predictions. If they can accurately foresee which Talented are dangerous they can also predict which are harmless, undermining the entire program of exterminating them all. And then there's a boatload of potential paradoxes that come out of the ability to see a future and trying to change it.
This manga is so fucking dumb.