Its one of many people not understanding the context of the quotes;
"He has the power to wipe out the entire human race and if we believe there is even a one percent chance that he is our enemy, we have to take it"
This does not mean that its an actual one percent chance, it is merely Batman justifying his actions by saying that the potential for Superman to turn on humanity should be considered and acted upon. This percentage for Superman to turn is in Batman's mind 100% when he's shown a vision of the future and told by a being from the future that he was always right about Batman.
While yes, the movie is absolutely terribly written and Batman doesn't have a logical reason for attacking Superman, only an emotional one, for a majority of the movie. You can understand where the quote was coming from
I tried to do it by proxy. Shoot the car they’re in, the car blows up or the grenade would go off in the guy’s hand, or when he shoots the tank and the guy pretty much lights the tank [himself]. I perceive it as him not killing directly, but if the bad guy’s are associated with a thing that happens to blow up, he would say that that’s not really my problem. - Zack Snyder
Its excuses like this one that you hear in court's, when a serial killer is trying to justify their actions. In this case, its murder because the intention is to recklessly endanger and kill, a majority of his actions being planned-out such as when he chooses to shoot the gas tank and burn a person alive. Remember when he planned to jump through the floor and attack an entire room of people? Well those actions were pre-meditated murder.
As @Wandering_Wind_Waffle explained here, Batman's actions are murders.
The issue is that because Batman kills, he has no reason to leave any of the rogues gallery alive. Why does he let Lex Luthor live who blew up a building with people inside - yet murders hired thugs who were likely just put somewhere and told to 'shoot at anything that comes through the doors'
The film has shot itself in the foot, in that we have no motivations that make sense. No real justification for the character's actions explained in the film and no reason why a lot of the problems between characters couldn't have been solved by just talking to one another. Civil War is going to tackle this, as it has Captain America and Iron Man try to talk multiple times throughout the film, even during fights one side is always shown in the trailers offering a chance for the other side to step down.