we are still with Martha ?
Batman believed Superman as an alien with God like powers taht can wipe out the entire human race. He wanted to erase him out of existence.
Bruce is always portrayed to be a paranoid, stubborn and a damaged man, who will do anything to safeguard his fellow humans.
The point to be noted here is that Bruce never believed or wanted to believe the fact that there would be a human side to Superman or a side where Superman really cares for every single human. When Clark utters those words, Bruce couldn't believe the fact that there is even a human side to him.
"Martha" is the last word Bruce heard from his father before his parents died at the alley -- the one incident that left a deep scar in his life and the only reason he started his crusade against crime in Gotham.
That was enough to give a pause to the hatred Bruce had it in him. And in that pause, Bruce realizes a few things that completely changes his perspective over who and what Superman is standing for. Quoting that line you mntioned as reference will help you understand the situation.
"He has the power to wipe out the entire human race. If we believe there is even a 1% chance that he is our enemy, we have to take it as an absolute certainty!"
Batman not believing in Superman as an alien is the key for him to believe that Superman is not an enemy for the humanity and that is enough to stop himself from killing Superman. And also everybody cared about the word Martha and nobody really saw what Superman really said.
"You are letting him kill Martha!"
Those were the exact words that made Bruce to realise a few things.
1.Superman was manipulated by somebody else who held "Martha" as a hostage.
2. Bruce realises that Superman too has humanity in him. Superman cares for a human so much that it makes him handcuff his true powers and fall him defeated at the hands of a human like Bruce. Bruce never misses to realise this! This makes him believe Superman is not the enemy of human race he thought him to be. He also realises that it was somebody else who set up Superman as a criminal for the bomb blast.
3. Bruce always thought, it was his fault that his parents died at the alley that night. He is shown having constant nightmares about his parants' death. Bruce never had a chace to undo that. When Clark utters those words, it affects Bruce so personally that it makes Bruce to go and help rescue Martha Kent from being a hostage. That was the moment of redemption Bruce had been awaiting his whole life. He never had a chance to save his parents: Thomas and Martha Wayne. He will not let, once again, Martha to die at the hands of another criminal. That's why he replies to Superman, "Martha will not die tonight!"
4. It was Luthor who pits both the heroes against one another. Lex exploits emotionally both the heroes and make them fight, in order to create enough distraction from stopping Superman interfering with his creation of Doomsday, that'd eventually succeed in killing Superman.
Batman's weakness is his rage and ego. Lex exploits exactly those rage and ego and makes Bruce to think Superman as an enemy to the whole human race.
Superman's weakness is his kindness. Lex exploits that too by threatening to kill Clark's mother by burning her as a witch. Unlike Bruce, Superman never wanted to kill Bruce. He just wanted to explain that situation he had been trapped into. Lex exploited Bruce's rage so much that Bruce never let Superman talk for even a second. Batman believes that his rage is the driving force that helps him inflict the fear in other criminals, but he realises after this fight that the rage he possessed was his weakness so far. Superman believes it is kindness that makes him more human but he never gave a second thought on whether others would exploit his kindness or not.
This is exactly how a fight between TWO TOO GOOD HEROES can end. Nobody is evil here. Both finds redemption here.
hinde parin ma gets ?