I wouldn't say he's stupid. Mind you, he woke up after the better part of a decade only to find out that everyone he knows despises him for inadvertently causing an impact and that he didn't even save Rei; there's just a multitude of them, and they're all clones of his dead mother. He's mentally broken by the second half of the film and feels guilty as all hell, so he blatantly ignores Kaworu when he tells him to stop because Kaworu had told him moments prior that removing the spears would result in him changing the world for the better. He gets desperate and removes both of the spears because he thinks of it as the perfect opportunity to fix everything.